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**Bioinformatics-II Computational Sciences April 2010
**

Prof. dr. Antoine van Kampen 1. Bioinformatics Laboratory, AMC 2. BioSystems Data Analysis, UvA a.h.vankampen@amc.uva.nl

Descriptive Statistics

Describing data

Moment

Non-mean based measure Mode, median Range (max-min), Interquartile range (1st3rd quartile) ---

Center Spread

Mean Variance (standard deviation) Skewness Kurtosis

Skew Peaked

Quartile

In descriptive statistics, a quartile is any of the three values which divide the sorted data set into four equal parts, so that each part represents 1/4th of the sample or population.

± first quartile (designated Q1) = lower quartile cuts off lowest 25% of data (25th percentile ) ± second quartile (designated Q2) = median cuts data set in half (50th percentile ) ± third quartile (designated Q3) = upper quartile cuts off highest 25% of data, or lowest 75% (75th percentile )

The difference between the upper and lower quartiles is called the interquartile range.

jerrydallal.Variance. the term degrees of freedom (df) is a measure of the number of independent pieces of information on which the precision of a parameter estimate is based.com/LHSP/dof. i !1 Degrees of freedom n 2 variance ( xi Q ) § n 1 ! s i !1 n 2 Standard deviation In statistics. S.D. http://www.htm Jack Good's 1973 article in the American Statistician "What are Degrees of Freedom?" 27. 227-228 . of a Sample ( xi Q ) 2 § n 1 ! s .

Skewness Frequency Value .

Box-whisker plots .

Quality of a sampling estimate Precision & validity No precision Precision but no validity Random error Systematic error (bias) .

hypergeometric. Poisson. chi-square What parameters describe their shapes How these distributions can be useful . binomial.Distributions Normal. t-distribution.

Normal distribution .

The Normal Distribution Also called a ³Gaussian´ distribution Centered around the mean Q with a width determined by the standard deviation W Total area under the curve = 1.0 1 ( x Q ) / 2W 2 f ( x) ! e W 2T .

. . For a mean of 5 and a standard deviation of 1: .A Normal Distribution .

The random uncertainty or random error . You won¶t get the same answer every time. a histogram of your measurements will approach the appearance of a normal distribution. ± Imagine repeating this process many times. but if you make a lot of measurements.What Does a Normal Distribution Describe? Imagine that you go to the lab and very carefully measure out 5 ml of liquid and weigh it. Any situation in which the exact value of a continuous variable is altered randomly from trial to trial.

the area under the curve between x=a and x=b is the probability that your next measurement of x will fall between a and b .How Do You Use The Normal Distribution? Use the area UNDER the normal distribution For example.

4 to 94.6 A normal distribution with a mean of 75 and a standard deviation of 10. The shaded area contains 95% of the area and extends from 55.4 75 94.55.6. .96 standard deviations of the mean. 95% of the area is within 1. For all normal distributions.

6 Area is determined by integration of normal distribution .4 94.55.

Integration .

How Do You Get Q and W? To draw a normal distribution you must know Q and W 1 ( x Q ) / 2W 2 f ( x) ! e W 2 If you made an infinite number of measurements. their mean would be Q and their standard deviation would be W In practice. you have a finite number of measurements with mean x and standard deviation s For now. Q and W will be given Later we¶ll use x and s to estimate Q and W .

The Standard Normal Distribution It is tedious to µintegrate¶ a new normal distribution for every population.Q) / W Use the standard normal distribution Q = 0 and W = 1 (areas tabulated in any statistics text book) The z-score indicates the number of standard deviations that value x is away from the mean Q . so use a µstandard normal distribution¶ with standard tabulated areas. Convert your measurement x to a standard score (z-score) z = (x .

Probability density function z-transform green curve is standard normal distribution .

Standard Normal Distribution z=1.5% .96 2.

Standard Normal Distribution .

66 .8% mean=0 std=1 x>=1.mean=5 std=3 x>=10 4.66 transform of mean: z = (5-5)/3 = 0 transform of other value: z = (10-5)/3 = 1.

What value would be needed to be in the 85th percentile? Stat tables: http://www.statsoft. what percent of the scores is: (a) greater than 30? (b) greater than 37? (c) between 28 and 34? *What proportion of a normal distribution is within one standard deviation of the mean? *What proportion is more than 1.8 standard deviations from the mean? *A test is normally distributed with a mean of 40 and a standard deviation of 7.com/textbook/sttable.Exercises 1 *If scores are normally distributed with a mean of 30 and a standard deviation of 5.html .

Binomial distribution .

What Does the Binomial Distribution Describe? yes/no experiments (two possible outcomes) The probability of getting all ³tails´ if you throw a coin three times The probability of getting all male puppies in a litter of 8 The probability of getting two defective batteries in a package of six .

Exercise 2 What is the probability of getting one µ2¶ when you roll six dice? .

k is a discrete variable ± Integer values only . if the overall probability of the result is p Note that here.The Binomial Distribution bionomial coefficient The probability of getting the result of interest k times out of n.

402 .Binomial Distribution n=6 p = 1/6 k = [0 1 2 3 4 5 6] number of dice rolled probability of rolling a 2 # of 2s out of 6 0.

k = [0 1 2 3 4 5 6 7 8].Binomial Distribution n = 8. p = 1/2. number of puppies in litter probability of any pup being male # of males out of 8 .

5 ± Approaches normal distribution if n is large.p) .The Shape of the Binomial Distribution Shape is determined by values of n and p ± Only truly symmetric if p = 0. unless p is very small Mean number of ³successes´ is np Variance of distribution is variance (X) = n p(1.

your little brother claims to have rolled a ³Yahtzee´ in 6¶s (five dice all 6¶s) in one roll of the five dice. How justified would you be in beating him up for cheating? .Exercise 3 While you are in the bathroom.

.. 2.) average of distribution variance == mean . 1.Poisson distribution e Q Pn ( Q ) ! n! P( ) Q n probability of getting n counts (=0..

Poisson distribution Randomly placed dots over 50 scale divisions. On average =1 dot per interval =1 e Q Pn (Q) ! n! P( ) Q n probability of getting n counts average of distribution n .

Exercise 4 e Q n (Q ) ! n! Q n Pn( ) probability of getting n counts average of distribution Average number of phone calls in 1 hour = 2.1 What is probability of getting 4 calls? .

1 What is probability of getting 0 calls? Does this simplify the formula? .Exercise 5 e Q n (Q ) ! n! Q n Pn( ) probability of getting n counts average of distribution Average number of phone calls in 1 hour = 2.

Hypergeometric distribution .

Then k balls are drawn from the urn without replacement and of these X are observed to be yellow. X is a random variable following hypergeometric distribution What is the probability of observing X=6 yellow balls? N=20 m=n=10 draw k=10 balls X=6 . of these m are yellow and others are blue.Hypergeometric Distribution Suppose that we have an urn with N balls in it.

00 0.15 2 4 X 6 8 10 P(X = x) = ¨m¸ ¨ n ¸ © ¹© ¹ ª x º ªk-xº ¨N¸ © ¹ ªkº N! x! (m-x)! (k-x)! (n-k+x)! = k! (N-k)! m! n! . 0 =n=k=10 White Balls drawn Remained in urn X m±X m Black k ±X n±k+X n k P(X) N-k N 0. 0.Hypergeometric Distribution N=20.

. it is less likely that we get the result by chance.Fisher¶s Exact Test We often want to ask whether there are more white balls in the sample than expected by chance. White Balls drawn Remained in urn x¶ m ± x¶ m Black k ± x¶ n ± k + x¶ n k N-k N P(X u x¶) = § ! x! (m-x)! (k-x)! ( -m-k x)! k! ( -k)! m! ( -m)! x= x' to min(m.k) If the probability is small.

Hypergeometric example We extracted 36 samples from leukemia microarray dataset: ± Whole dataset: 47 ALL + 25 AML (total 72 samples) How many ALL and AML samples do you expect when you randomly select samples from the dataset? .

5 ALL 12.88 (original ratio = 47/25=1.5 AML ratio = 1.Hypergeometric example We extracted 36 samples from leukemia microarray dataset: ± Whole dataset: 47 ALL + 25 AML (total 72 samples) How many ALL and AML samples do you expect when you randomly select samples from the dataset? Answer: 23.88) .

Hypergeometric example We extracted 36 samples from leukemia microarray dataset: ± Whole dataset: 47 ALL + 25 AML (total 72 samples) ± Extracted: 29 ALL + 7 AML Is this sample enriched for ALL samples? ALL Extracted Not extracted Total: 29 18 47 AML 7 18 25 36 36 72 Pr(extracted ALL 29) ¨47¸ ¨ 25 ¸ ª i º ª36 ± iº = ¨ 72 ¸ i >= 29 ª 36 º § 36 = 0.006 Conclusion: This sample is significantly enriched with ALL samples possible bias in sample selection .

a statistic is a random variable). A sampling distribution is a distribution that describes the chance fluctuations of a statistic calculated from a random sample.Sampling Distribution Every time we take a random sample and calculate a statistic. If we continue to take random samples and calculate a given statistic over time. we will build up a distribution of values for the statistic. . This distribution is referred to as a sampling distribution. the value of the statistic changes (remember.

**Sampling Distribution of the Mean
**

The probability distribution of distribution of the mean.

X

is called the sampling

The distribution of X , for a given sample size n, describes the variability of sample averages around the population mean .

**Sampling Distribution of the Mean
**

If a random sample of size n is taken from a normal 2 population having mean x and varianceW x , then X is a random variable which is also normally distributed with mean x and variance W 2 .

x

n

Further,

X Qx Z! W n

is a standard normal random variable.

**Sampling Distribution of the Mean
**

Original population 1

Original Population Averages - Sample Size = 10

n(100,5)

3

n(100,1.58)

80

85

90

95

100 X

105

110

115

120

80

85

90

95

100 X(10)

105

110

115

120

Averages - Sample Size = 2

Averages - Sample Size = 25

2

n(100,3.54)

4

n(100,1)

5/sqrt(2)=3.54

80 85 90 95 100 X(2) 105 110 115 120

80 85 90 95 100 X(25) 105 110 115 120

**Sampling Distribution of the Mean
**

Example: A manufacturer of steel rods claims that the length of his bars follows a normal distribution with a mean of 30 cm and a standard deviation of 0.5 cm.

(a) Assuming that the claim is true, what is the probability that a given bar will exceed 30.1 cm? (b) Assuming the claim is true, what is the probability that the mean of 10 randomly chosen bars will exceed 30.1 cm? (c) Assuming the claim is true, what is the probability that the mean of 100 randomly chosen bars will exceed 30.1 cm?

Sampling Distribution of the Mean Example: A manufacturer of steel rods claims that the length of his bars follows a normal distribution with a mean of 30 cm and a standard deviation of 0.5=0.1 cm? (z=30.1 cm? (z=30.5/sqrt(100)=2 p=0.2 p=0.63 p=0. what is the probability that the mean of 10 randomly chosen bars will exceed 30.42) (b) Assuming the claim is true. (a) Assuming that the claim is true. what is the probability that the mean of 100 randomly chosen bars will exceed 30.5/sqrt(10)=0.1-30)/0.1-30)/(0.26) (c) Assuming the claim is true. what is the probability that a given bar will exceed 30.5 cm.1 cm? (z=30.1-30)/(0.02) .

Sampling Distribution of the Mean Steel Bar Lengths (cm) .5 30 X(100) 30.5 29 29.42 28.5 29 29.02 28.5 29 29.5 31 31.5 .5 30 X 30.5 28.5 30 X(10) 30. 26 .5 Steel Bar Lengths (cm) Steel Bar Lengths (cm) .5 31 31.5 31 31.

standard error: _ W x = W .Properties of Sample Mean as Estimator of Population Mean Expected value of sample mean is population mean X) ! Q The mean has variance Variance = W 2 n n As n increase. _ W x decrease.

.

5 X .When the Population is Normal then the Sampling Distribution is Also Normal Population Distribution Central Tendency = 10 Q _ = Q x Q = 50 X Variation W _ = W x n Sampling Distributions n=4 DX = 5 QX = 50 X n =16 DX = 2.

Central Limit Theorem As Sample Size Gets Large Enough Sampling Distribution Becomes almost normal regardless of shape of population X X .

When The Population is Not Normal Population Distribution Central Tendency W = 10 Q = 50 X Sampling Distributions n=4 WDX = n =30 WDX = 1.8 Q _ = Q x Variation W _ = W x n QX ! 50 X .

If n < 30.Central Limit Theorem Rule of thumb: normal approximation for X will be good if n > 30. Otherwise t-distribution . the approximation is only good if the population from which you are sampling is not too different from normal.

t-Distribution So far. we have been assuming that we knew the value of . However. it is often true that one is estimating from the same set of data. along with §(Xi X ) W !s! Ö n 1 2 . This may be true if one has a large amount of experience with a certain process.

t-Distribution To allow for such a situation. S n standard error of the mean . we will consider the t statistic: X Qx T! S n which follows a t-distribution.

t-Distribution t-Distribution t(n=6) t(n=g) = Z t(n=3) -4 -3 -2 -1 0 t 1 2 3 4 .

where is degrees of freedom. and §(Xi X ) S ! 2 2 then n 1 X Q t! S/ n is a random variable following the t. .t-Distribution If X is the mean of a random sample of size n taken from a normal population having the mean and variance 2.distribution with parameter = n ± 1.

05 . t1.20 t.t-Distribution The t-distribution has been tabularized. due to symmetry. Note. t represents the t-value that has an area of it.= -t t-Distribution to the right of -4 -3 -2 -1 0 t(n=3) 1 2 3 4 t.95 t.80 t.

We sample 5 batches and get the following readings: 1400. 1450. 1375. X ! 1455 S ! 72 Does this data support or refute a population average of 1400? . 1550. 1500.Example: t-Distribution The resistivity of batches of electrolyte follow a normal distribution.

025 Refute 3 4 1.71 S/ n 72 / 5 t-Distribution Support Refute -4 -3 -2 -1 0 t(n=5) 1 2 p=0.Example: t-Distribution X Q 1455 1400 t! ! ! 1.71 t=2.78 .

Introduction to Hypothesis Testing .

Nonstatistical Hypothesis Testing« A criminal trial is an example of hypothesis testing without the statistics. In a trial a jury must decide between two hypotheses. The null hypothesis is H0: The defendant is innocent The alternative hypothesis or research hypothesis is H1: The defendant is guilty The jury does not know which hypothesis is true. They must make a decision on the basis of evidence presented.

Nonstatistical Hypothesis Testing« In the language of statistics convicting the defendant is called rejecting the null hypothesis in favor of the alternative hypothesis.

± That is, the jury is saying that there is enough evidence to conclude that the defendant is guilty (i.e., there is enough evidence to support the alternative hypothesis).

** If the jury acquits it is stating that there is not enough evidence to support the alternative hypothesis.
**

± Notice that the jury is not saying that the defendant is innocent, only that there is not enough evidence to support the alternative hypothesis. ± That is why we never say that we accept the null hypothesis.

Nonstatistical Hypothesis Testing« There are two possible errors. A Type I error occurs when we reject a true null hypothesis. That is, a Type I error occurs when the jury convicts an innocent person. A Type II error occurs when we don¶t reject a false null hypothesis. That occurs when a guilty defendant is acquitted.

Nonstatistical Hypothesis Testing« The probability of a Type I error is denoted as . The probability of a type II error is . The two probabilities are inversely related. Decreasing one increases the other.

Conclude that there is not enough evidence to support the alternative hypothesis. There are two possible decisions: ± ± Conclude that there is enough evidence to support the alternative hypothesis. 3. The procedure begins with the assumption that the null hypothesis is true. . 3. There are two hypotheses. 2. the null and the alternative hypotheses. 4.Nonstatistical Hypothesis Testing« The critical concepts are these 1. The null hypothesis (H0) will always state that the parameter equals the value specified in the alternative hypothesis (H1) The goal is to determine whether there is enough evidence to infer that the alternative hypothesis is true.

hypothesis) about a parameter is supported by the data.e. . Population Sample Inference Statistic Parameter Hypothesis testing allows us to determine whether enough statistical evidence exists to conclude that a belief (i. Hypothesis testing is a procedure for making inferences about a population.

Concepts of Hypothesis Testing« Example: mean demand for computers during assembly lead time. our operations manager wants to know whether the mean is different from 350 units. Rather than estimate the mean demand. our research hypothesis becomes: H1: 350 This is what we are interested in determining . We can rephrase this request into a test of the hypothesis: H0: = 350 Thus.

Thus. we will assume: H0: = 350 (assumed to be TRUE) .Concepts of Hypothesis Testing« The testing procedure begins with the assumption that the null hypothesis is true. until we have further statistical evidence.

Concepts of Hypothesis Testing« The goal of the process is to determine whether there is enough evidence to infer that the alternative hypothesis is true. is true? This is what we are interested in determining . That is. is there sufficient statistical information to determine if this statement: H1: 350.

Concepts of Hypothesis Testing« There are two possible decisions that can be made: Conclude that there is enough evidence to support the alternative hypothesis (also stated as: rejecting the null hypothesis in favor of the alternative) Conclude that there is not enough evidence to support the alternative hypothesis (also stated as: not rejecting the null hypothesis in favor of the alternative) NOTE: we do not say that we accept the null hypothesis. .

600) would provide enough evidence. For example. the next step is to randomly sample the population and calculate a test statistic (in this example. if we¶re trying to decide whether the mean is not equal to 350. . a large value of (say. 355) we could not say that this provides a great deal of evidence to infer that the population mean is different than 350. the sample mean). If the test statistic¶s value is inconsistent with the null hypothesis we reject the null hypothesis and infer that the alternative hypothesis is true.Concepts of Hypothesis Testing« Once the null and alternative hypotheses are stated. If is close to 350 (say.

. There are probabilities associated with each type of error: P(Type I error) = P(Type II error ) = is called the significance level.Concepts of Hypothesis Testing« Two possible errors can be made in any test: ± A Type I error occurs when we reject a true null hypothesis and ± A Type II error occurs when we don¶t reject a false null hypothesis.

Types of Errors« A Type I error occurs when we reject a true null hypothesis (i.e. Reject H0 when it is TRUE) A Type II error occurs when we don¶t reject a false null hypothesis (i.e. Do NOT reject H0 when it is FALSE) .

The accounts are approximately normally distributed with a standard deviation of ¼65. A random sample of 400 monthly accounts is drawn. Can we conclude that the new system will be cost-effective? .Example A department store manager determines that a new billing system will be cost-effective only if the mean monthly account is more than ¼170. for which the sample mean is ¼178.

our null hypothesis becomes: H0: = 170 (this specifies a single value for the parameter of interest) . We express this belief as a our research hypothesis.Example The system will be cost effective if the mean account balance for all customers is greater than ¼170. that is: H1: > 170 (this is what we want to determine) Thus.

Example What we want to show: H1: > 170 H0: = 170 (we¶ll assume this is true) We know: n = 400 = 178 = 65 Hmm. What to do next?! .

We will explore both in turn« . and The p-value approach (which is generally used with a computer and statistical software). we can use two different approaches: The rejection region approach (typically used when computing statistics manually).Example To test our hypotheses.

.Example. is the critical value of to reject H0. Rejection Region« The rejection region is a range of values such that if the test statistic falls into that range. we decide to reject the null hypothesis in favor of the alternative hypothesis.

= P( > ) is also« = P(rejecting H0 given that H0 is true) = P(Type I error) . that is if > .Example It seems reasonable to reject the null hypothesis in favor of the alternative if the value of the sample mean is large relative to 170.

Example All that¶s left to do is calculate and compare it to 178. we can calculate this based on any level of significance ( ) we want« .

we reject the null hypothesis in favor of H1. that: > 170 and that it is cost effective to install the new billing system .e.05). =0.Example At a 5% significance level (i. i.e. we get Solving we compute =175.34).34 Since our sample mean (178) is greater than the critical value we calculated (175.

Example The Big Picture« H1: > 170 H0: = 170 Reject H0 in favor of =175.34 =178 .

05).Standardized Test Statistic« An easier method is to use the standardized test statistic: and compare its result to : (rejection region: z > ) Since z = 2.46 > 1.645 (z. we reject H0 in favor of H1« .

what is the probability of observing a sample mean at least as extreme as the one already observed (i.p-Value The p-value of a test is the probability of observing a test statistic at least as extreme as the one computed given that the null hypothesis is true. In the case of our department store example. given that the null hypothesis (H0: = 170) is true? p-value .e. = 178).

We observe a p-value of .0069. hence there is evidence to support H1: > 170. the more statistical evidence exists to support the alternative hypothesis.Interpreting the p-value« The smaller the p-value. .

10 .05 .Interpreting the p-value« Overwhelming Evidence (Highly Significant) Strong Evidence (Significant) Weak Evidence (Not Significant) No Evidence (Not Significant) 0 p=.01 .0069 .

Interpreting the p-value« Compare the p-value with the selected value of the significance level: If the p-value is less than . we judge the p-value to be small enough to reject the null hypothesis. Since p-value = . If the p-value is greater than . we reject H0 in favor of . we do not reject the null hypothesis.05.0069 < H1 = .

the parameter to be tested is the population mean. the alternative hypothesis is H1: < 22 The null hypothesis is H0: = 22 . Thus. Thus.Another example« The objective of the study is to draw a conclusion about the mean payment period. We want to know whether there is enough statistical evidence to show that the population mean is less than 22 days.

. As a result we locate the rejection region in the left tail of the sampling distribution. We set the significance level at 10%.Another example« The test statistic is z! x Q W/ n We wish to reject the null hypothesis in favor of the alternative only if the sample mean and hence the value of the test statistic is small enough.

759 ! ! 21 . 63 220 §x x ! 220 and z! x Q / n ! 21.91 p-value = P(Z < -.63 22 6 / 220 ! .1814 Conclusion: There is not enough evidence to infer that the mean is less than 22. .28 4 .10 ! 1.Another example« Rejection region: Assume z i z E ! z.91) =0.

because the rejection region is located in only one tail of the sampling distribution: More correctly. this was an example of a right tail test.One± and Two±Tail Testing« The department store example was a one tail test. .

.One± and Two±Tail Testing« The µpayment period¶ example is a left tail test because the rejection region was located in the left tail of the sampling distribution.

Right-Tail Testing« Calculate the critical value of the mean ( ) and compare against the observed value of the sample mean ( )« .

Left-Tail Testing« Calculate the critical value of the mean ( ) and compare against the observed value of the sample mean ( )« .

Two±Tail Testing« Two tail testing is used when we want to test a research hypothesis that a parameter is not equal () to some value .

87 (respectively).09 . They then sample 100 customers at random and recalculate a monthly phone bill based on competitor¶s rates.09 and ¼3. We do this by assuming that: H0: = 17. What we want to show is whether or not: H1: 17. They calculate the mean and standard deviation for all their customers at ¼17.Example KPN argues that its rates are such that customers won¶t see a difference in their phone bills between them and their competitors.09.

so we divide this probability by 2. we set up a two-tail rejection region. The total area in the rejection region must sum to . .Example The rejection region is set up so we can reject the null hypothesis when the test statistic is large or when it is small. stat is ³small´ stat is ³large´ That is.

96 -z.05). = . z.Example At a 5% significance level (i.e.025 z . we have /2 = .96 and our rejection region is: z < ±1.025. Thus.025 = 1.96 -orz > 1.025 0 +z.

55 Using our standardized test statistic: We find that: Since z = 1.Example From the data. nor less than ±1.19 is not greater than 1. There is insufficient evidence to infer that there is a difference between the bills of KPN and the competitor. .96.96 we cannot reject the null hypothesis in favor of H1. we calculate = 17.

and Two-Tail Tests« One-Tail Test (left tail) Two-Tail Test One-Tail Test (right tail) .Summary of One.

34) . ± how the probability of a Type II error is calculated ± its interpretation.Probability of a Type II Error ± It is important that that we understand the relationship between Type I and Type II errors. Recall previous example H0: = 170 H1: > 170 At a significance level of 5% we rejected H0 in favor of H1 since our sample mean (178) was greater than the critical value of (175.

34 (our critical value) we will not reject our null hypothesis.34 given that the null hypothesis is false) . we can see that: = P( < 175. which means that we will not install the new billing system. Thus.Probability of a Type II Error ± A Type II error occurs when a false null hypothesis is not rejected. In our example this means that if is less than 175.

For example.34. thus« . given that = 180). = P( < 175.Example = P( < 175. suppose the true mean account balance is ¼180.34 given that the null hypothesis is false) We need to compute for some new value of .

Example Our original hypothesis our new assumption .

increases the value of Decreasing the significance level and vice versa.Effects on of Changing . Consider this diagram again. Shifting the critical value line to the right (to decrease ) will mean a larger area under the lower curve for « (and vice versa) .

both of which are selected by the statistics practitioner.Judging the Test« A statistical test of hypothesis is effectively defined by the significance level ( ) and the sample size (n). and/or increasing the sample size. Therefore. we can reduce it by increasing . if the probability of a Type II error ( to be too large. ) is judged . n.

Judging the Test« For example.000« The probability of a Type II error ( level while remains at 5% ) goes to a negligible . suppose we increased n from a sample size of 400 account balances to 1.

.Judging the Test« The power of a test is defined as 1± . It represents the probability of rejecting the null hypothesis when it is false.

F (POWER) F .E Reject E 100 .Error Rates and Power (H0 and H1 = null and alternative hypothes) Fate of H0 Accept H0 Actually True H1 100 .

Factors Affecting Power Increasing overall sample size increases power Having unequal group sizes usually reduces power Larger size of effect being tested increases power Setting lower significance level decreases power Violations of assumptions underlying test often decrease power substantially .

Exercises Exercises z-test (see word document) .

The t-test .

W2) population.Recall t distribution. . ± This statistic follows a t distribution with n-1degrees of freedom. Consider X Q . X Q W n has a standard normal distribution. S is not expected to be close to W. Take random sample of size n from a N(Q. S introduces additional variability. Thus this statistic will be more variable that a standard normal random variable. S n ± This is approximately normal if n is large. ± If n is small.

Confidence Intervals. Suppose that the population is normally distributed with mean Q and variance W2. a 100(1-E)% confidence interval for Q is. xsz /2 W n ± If W is not known. x s tE / 2 (n 1) s n . Then ± If W is known. a 100(1-E)% confidence interval for Q is.

one for a single sample and one for two samples. The one sample t-test is used to test whether a population has a specific mean value The two sample t-test is used to test whether population means are equal. e. There are two main forms of the t-test. .Overview of the t-test The t-test is used to help make decisions about population values. do training and control groups have the same mean..g.

75/sqrt(50) = . For example.63.81. Then we find the standard error of the mean by dividing SD by sqrt(N) = 5. The critical value of t with (50-1) df is 2.05 inches. Our confidence interval is.One-sample t-test We can use a confidence interval to ³test´ or decide whether a population mean has a given value.75 inches. We find that their mean height is 63. . We randomly sample 50 women students at USF. 63. alpha=0.025).05 plus/minus 1. suppose we want to test whether the mean height of women at University of South Florida (USF) is less than 68 inches.01(find this in a t-table. therefore. The SD of height in the sample is 5.

01 4 Frequenc ci ! X s 1.75 6 S X ! .One-sample t-test example ne sample t test Confi ence inter al ei 10 N=50 8 Pop Mean = 68 M = 63.8 1 Histogram of Sample Height t=2. Does the interval contain the hypothesized value? ¡ Hei t i I c es in Inc .63 2 0 40 50 60 70 80 Take a sample. set a confidence interval around the sample mean.05 SD=5.

it is very. If the population mean is really 68 inches. .One-sample t-test Example ne sample t test t istri ution iew 15 X ! 63. Errors) from the hypothesized population mean.8 1 SX 6 Frequenc 3 0 62 Height in Inches 70 The sample mean is roughly six standard deviations (St.05 inches.8 1 4 . very unlikely that we would find a sample with a mean as small as 63.1 1 t ! .05 12 Q ! 68 t istri ution X Q ! 4.95 9 S X ! .9 5 X Q ! ! 6 .

control group ± Males vs.g. ± means are just the same or different (nondirectional) ± or can predict one group higher (directional). females ± New training vs.Two-sample t-test Used when we have two groups. e.. ± Experimental vs. . old training method Tests whether group population means are the same.

We will then have a sampling distribution of mean differences. Then we subtract the mean for group 1 from the mean for group 2. The standard deviation of the sampling distribution will be: 2 2 W X1 X 2 ! W X1 W X 2 The standard error of the difference is the root of the sum of squared standard errors of the mean. If the two groups are sampled at random from 1 population. We measure the height of each person and find the mean for each group. .Sampling Distribution of Mean Differences Suppose we sample 2 groups of size 50 at random from USF. the mean of the differences in the long run will be zero because the mean for both groups will be the same. Suppose we do this over and over.

We would expect that the average mean difference would be zero. What would the standard deviation of the distribution of differences be? SD 2 36 2 ! 100 WX ! N SD ! 6 / 10 ! .6. for the difference in means.6 WX ! N W X1 X 2 ! W 2 X1 W 2 X2 36 36 72 ! ! ! . Suppose we sampled people 100 at a time into two groups. it is .85 100 100 100 The standard error for each group mean is .85. .Example of the Standard Error of the Difference in Means Suppose that at USF the mean height is 68 inches and the standard deviation of height is 6 inches.

Estimating the Standard Error of Mean Differences The USF scenario we just worked was based on population information. thus: S X1 X 2 ! S S S 2 2 here S X ! N 2 X1 2 X2 All this says is that we replace the population variance of error with the appropriate sample estimators. . That is: 2 2 W X1 X 2 ! W X1 W X 2 We generally don¶t have population values. We usually estimate population values with sample data.

When the sample sizes are not equal across groups. we find the pooled standard error. The pooled standard error is a weighted average. where the weights are the groups¶ degrees of freedom. S X1 X 2 2 (n1 1) s12 (n2 1) s2 ¨ 1 1 ¸ © ¹ ! (n1 1) (n2 1) © n1 n2 ¹ ª º .Pooled Standard Error S X1 X 2 ! S S 2 X1 2 X2 We can use this formula when the sample sizes for the two groups are equal.

.Back to the Two-Sample t The formula for the two-sample t-test for independent samples looks like this: t X1 X 2 X1 X 2 ! S X1 X 2 This says we find the value of t by taking the difference in the two sample means and dividing by the standard error of the difference in means.

we just want to know if there is a difference. Scores come from comparing what people guess to what the people in the films said they felt at the time. So we find some (N=15) of each major and give each the test. . The test has people view film clips and guess what people in the clips are feeling. Empathy by College Major Suppose we have a professionally developed test of empathy. We want to know whether Psychology majors have higher scores on average to this test than do Physics majors.Example of the two-sample t. No direction.

Empathy Scores Person 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Psychology 10 12 13 10 8 15 13 14 10 12 10 12 13 10 8 Physics 8 14 12 8 12 9 10 11 12 13 8 14 12 8 12 .

20 4. .87 2.05>.292+.38/15=.46/.323) .87 Sqrt(.05 Term X1 X 2 S X1 X 2 t df t(.33 2.59 28 X1 X 2 ! S X1 X 2 Psychology 15 11.46 .33-10.78 . 28 df) 2 tail 2.84 .59.Empathy From data N Mean SD SD2 2 SX t X1 X 2 Physics 15 10.323 Result .38 4. n.09 4.292 Calculation 11.s.05.78 15+15-2 2.

Exercise Exercises t-test. see word document .

Chi-square .

O2. Ek. . Sum of the observed frequencies is n. 2. O3. frequencies: E1. O1 O2 O3 . . Expected.Background: 1. Ok. kth k k Total n n . « . Each observation falls into a cell (or class). or theoretical. . 3. Suppose there are n observations. E3. E2. Observed frequencies in each cell: O1. . Ok ! n 4. 1 2 3 . . . k !n 1st bserved Frequency xpected Frequency 1 1 k ategories 2nd 3rd 2 2 3 3 .

Goal: 1. Large values of G2: Observed frequencies do not agree with expected frequencies. . Compare the observed frequencies with the expected frequencies. Decide whether the observed frequencies seem to agree or seem to disagree with the expected frequencies. 2. Methodology: Use a chi-square statistic: (O E ) 2 G2 ! § E all cells Small values of G2: Observed frequencies close to expected frequencies.

Sampling Distribution of G2*: When n is large and all expected frequencies are greater than or equal to 5. 2. G2 is nonnegative in value. G2 is not symmetrical. a separate distribution for each different number of degrees of freedom. . it is skewed to the right. then G2* has approximately a chi-square distribution. G2 is distributed so as to form a family of distributions. it is zero or positively valued. 3. Recall: Properties of the Chi-Square Distribution: 1.

Critical values for chi-square: 1. Chi-square distribution is not symmetrical: critical values associated with right and left tails are given separately. E 0 G 2 (df . 2. 3. 4. Identified by degrees of freedom (df) and the area under the curve to the right of the critical value. See Table. E ) G2 . E): critical value of a chi-square distribution with df degrees of freedom and E area to the right. G2(df.

3 .Example: Find G2(16.05 26.3 . / 16 / G2(16.05 0 G 2 (16.05) G2 Portion of Table Area to the right df .05). 0.05) = 26. 0. 0.0. 0.

. Use a one-tailed critical region. . . H0: The probabilities p1. pk are correct. 5. p2. 4. Expected frequencies: Ei ! n pi 6.Testing Procedure: 1. the right-hand tail. Test statistic: E all cells 3. Degrees of freedom: df = k 1. To ensure a good approximation to the chi-square distribution: Each expected frequency should be at least 5 ( Ei u 5). Ha: At least two probabilities are incorrect. . (O E)2 G2 ! § 2. .

05. A sample of 100 consumers tried each cereal and indicated the cereal he or she preferred. or did they indicate each cereal was equally likely to be selected? Use E = 0.Example: A market research firm conducted a consumer-preference experiment to determine which of 5 new breakfast cereals was the most appealing to adults. The results are given in the following table: Cereal Frequency A 25 B 17 C 15 D 22 E 21 Total 100 Is there any evidence to suggest the consumers had a preference for one cereal. .

05. if no preference is given. Thus. The null and alternative hypotheses: H0: There was no preference shown (equally distributed). The Set-up: a. 2.2) = 20 consumers in each class. b. we expect the 100 consumers to be equally distributed among the 5 cereals. b. Population parameter of concern: Preference for each cereal. The Hypothesis Test Criteria: a.Solution: If no preference was shown. 1. Test statistic: G2* with df = k 1 = 5 1 = 4 c. the probability that a particular cereal is selected. Ha: There was a preference shown (not equally distributed). Assumptions: The 100 consumers represent a random sample. . Level of significance: E = 0. we expect (100)(0.

25 0.05 3. Calculate the value of the test statistic: O 25 17 15 22 21 100 G2 = 3.25 0.20 .20 0. b.2 E 20 20 20 20 20 100 O E 5 -3 -5 2 1 0 (O E )2/E 1. Sample information: Table given in the statement of the problem. The Sample Evidence: a.45 1.3.

The Results: a. there is no evidence to suggest the consumers showed a preference for any one cereal. The p-value: ! P ( G 2 * " 3. 0. Decision: Fail to reject H0. b. The p-value is larger than the level of significance. 0. The Probability Distribution (Classical Approach): a. The Probability Distribution (p-Value Approach): a.2 | df ! 4). G2* is not in the critical region. 5. Critical value: G2(k 1.49 b.05) = G2(4. . E. 6.05 level of significance. b.4.5429. Using computer: P = 0. Conclusion: At the 0.05) = 9.

C2. 4. . Cc: marginal totals. R1. 2. c: number of columns. . Ei . . r: number of rows. R2. j Row total v Column tot al Ri v C j ! ! n Grand total Each Ei. .r v c Contingency Table: 1. Expected frequency in the ith row and the jth column: 3. . . Degrees of freedom: d ! ( r 1) (c 1) n = grand total. Rr and C1. . . 5. Used to test the independence of the row factor and the column factor.j should be at least 5. 6.

59) 10 16 15 41 (17.16 E all cells 2 .77) (12.03) (12.72) 61 39 45 145 (O E ) 2 G *! § ! 14.98) (15.64) (14.Contingency table showing sample results and expected values: Tax Reform Yes No Unsure Total Political Party Democrat Republican Independent Total 34 11 12 57 (23.25) (11.69) 17 12 18 47 (19.33) (17.

The Probability Distribution (p-Value Approach): a.16 | df ! 4) By computer: P = 0. The p-value: ! P ( G 2 * " 14. b. 0. Critical value: G2(4. .0068. 4.3 b. The Results: a. The p-value is smaller than the level of significance. The Probability Distribution (Classical Approach): a. b. Decision: Reject H0.4.01) = 13. Conclusion: There is evidence to suggest that opinion on tax reform and political party are not independent. 5. G2* is in the critical region. E.

ANOVA Analysis of Variance .

you learned how to use the t distribution to test the hypothesis of no difference between two population means. Suppose. however.From t to F« In the independent samples t test. that we wish to know about the relative effect of three or more different ³treatments´? .

± It is tedious to compare all possible combinations of groups. However. ± There are so many comparisons that some will be significant by chance.From t to F« We could use the t test to make comparisons among each possible combination of two means. this method is inadequate in several ways. . ± Any statistic that is based on only part of the evidence (as is the case when any two groups are compared) is less stable than one based on all of the evidence.

Such an overall test of significance is the F test. or ANOVA. or the analysis of variance. there will be no point in searching further.From t to F« What we need is some kind of survey test that will tell us whether there is any significant difference anywhere in an array of categories. If it tells us no. .

This question about means is answered by analyzing variances.The logic of ANOVA Hypothesis testing in ANOVA is about whether the means of the samples differ more than you would expect if the null hypothesis were true. you are asking about the variances among those means. you focus on variances because when you want to know how several means differ. ± Among other reasons. .

**Two Sources of Variability
**

In ANOVA, an estimate of variability between groups is compared with variability within groups. ± Between-group variation is the variation among the means of the different treatment conditions due to chance (random sampling error) and treatment effects, if any exist. ± Within-group variation is the variation due to chance (random sampling error) among individuals given the same treatment.

ANOVA

Total Variation Among Scores

Within Groups Variation Variation due to chance.

Between Groups Variation Variation due to chance and treat ent effect (if any exi ti .

Variability Between Groups

There is a lot of variability from one mean to the next. Large differences between means probably are not due to chance. It is difficult to imagine that all six groups are random samples taken from the same population. The null hypothesis is rejected, indicating a treatment effect in at least one of the groups.

Variability Within Groups

Same amount of variability between group means. However, there is more variability within each group. The larger the variability within each group, the less confident we can be that we are dealing with samples drawn from different populations.

The F Ratio

Between GroupVariability F! Within GroupVariability

ANOVA (F)

Total Variation Among Scores Within- roups Variation Variation due to chance. Between- roups Variation Variation due to chance and treatment effect (if any existis).

**Two Sources of Variability
**

Variabilit y Bet een Groups ! Variabilit y Within Groups

F

1

**Two Sources of Variability
**

Variabilit y Bet een Groups ! Variabilit y Within Groups

F !1

The F Ratio

ANOVA (F)

Total Variation Among Scores Within- roups Variation Variation due to chance. Between- roups Variation Variation due to chance and treatment effect (if any existis).

Mean Squares Within

Mean Squares Between

MSbetween F! MSwithin

mean squares between mean squares within

The F Ratio

MSbetween F! MSwithin

sum of squares within sum of squares between

MSwithin

SSwithin ! dfwithin

MSbetween

SSbetween ! df between

degrees of freedom within

degrees of freedom between

s !

2

§(X X)

n 1

2

Sum of Squares Degrees of Freedom

The F Ratio MSbetween F! MSwithin MSwithin SSwithin ! dfwithin sum of squares total MSbetween SSbetween ! df between SStotal ! SSbetween SSwithin degrees of freedom total dftotal ! dfbetween dfwithin .

then 2 2 T G square the total) een !7 n N Total number of subjects. scores together. and divide by the number of Grand Total (add all of the subjects in the group. .The F Ratio: SS Between SS between ! n7( X group X grand ) 2 SS bet Find each group total. square it.

2 SS within ! 7X 7 2 Squared group total. . n Number of subjects in each group.The F Ratio: SS Within 2 SS within ! 7( X X group ) Square each individual score and then add up all of the squared scores.

. Total number of subjects. then add all of the squared scores together. then square the total) Square each score.The F Ratio: SS Total SS total ! 7( X X grand ) 2 ! ( X group X grand ) ( X X group ) SStotal G ! §X N 2 2 Grand Total (add all of the scores together.

using the .An Example: ANOVA A study compared the intensity of pain among three groups of treatment. Treatment 1 7 6 5 6 Treatment 2 12 8 9 11 Treatment 3 8 10 12 10 . Determine the significance of the difference among groups.05 level of significance.

An Example: ANOVA State the research hypothesis. ± Do ratings of the intensity of pain differ for the three treatments? State the statistical hypothesis. H 0 : Q1 ! Q 2 ! Q3 H A : H 0 is false. .

. A directional test is possible only in situations where there are only two ways (directions) that the null hypothesis could be false. H0 may be false in any number of ways. all may be different. a distinction was made between directional and nondirectional alternative hypotheses. Such a distinction no longer makes sense when the number of means exceeds two. ± Two or more group means may be alike and the remainder differ.Nondirectional Test In testing the hypothesis of no difference between two means. and so on.

df within ! total number o sub ects ...total number o groups .1 Within: df within ! n1 1 n 2 1 n3 1.Degrees of Freedom Between: df between ! number o groups .

An Example: ANOVA Set decision rule.05 df between ! number o groups 1 ! 3 1 ! 2 df within ! ( n1 1) ( n 2 1) ( n3 1) ! ( 4 1) ( 4 1) ( 4 1) ! 9 . E ! .

05 df between ! 2 df within ! 9 Fcrit ! 4.An Example: ANOVA Set the decision rule. E ! .26 .

An Example: ANOVA Calculate the test statistic. Treatment A 7 6 5 6 T:24 49 36 25 36 146 X2 Treatment B 12 8 9 11 T:40 144 64 81 121 410 X2 Treatment C 8 10 12 10 T:40 64 100 144 100 408 X2 SS within T2 ! 7X 7 n 2 Grand Total: 104 SS within « 24 2 40 2 40 2 » ! 146 410 408 ¬ 144 ¼ ! 964 ? 400 400A ! 20 4 4 4 ½ .

An Example: ANOVA Calculate the test statistic.33 ! 42. Treatment A 7 6 5 6 T:24 49 36 25 36 146 X2 Treatment B 12 8 9 11 T:40 144 64 81 121 410 X2 Treatment C 8 10 12 10 T:40 64 100 144 100 408 X2 SS between T 2 G2 !7 n N Grand Total: 104 SS between 24 2 40 2 40 2 (104) 2 ! ! 144 400 400 901.67 4 4 4 12 .

67 ! ! ! 21.34 df between 2 SS within 20 ! ! ! 2.34 ! ! ! 9.61 MS within 2.22 .22 df within 9 MS between 21.An Example: ANOVA MS between ! MS within MS between MS within SS between 42.

ANOVA Summary Table ± In the literature.34 2.67 MS 21.61 .An Example: ANOVA Determine if your result is significant. ± There is a significant difference between the treatments.26 Interpret your results. 9.22 F 9. ± Reject H0.61>4. the ANOVA results are often summarized in a table. Source Between Groups Within Groups Total df 2 9 11 SS 42.67 20 62.

Post hoc tests have been designed for doing pair-wise comparisons after a significant F is obtained. that there is a real difference somewhere among our means. . with some degree of confidence. we don¶t know where that difference is. But if there are more than two groups. we know.After the F Test When an F turns out to be significant.

± The 5 participants in the ³famous´ condition are led to believe that these are each famous paintings.Exercise 6: ANOVA A psychologist interested in artistic preference randomly assigns a group of 15 subjects to one of three conditions in which they view a series of unfamiliar abstract paintings. Does what people are told about paintings make a difference in how well they are liked? Use the . Famous 10 7 5 10 8 Critically Acclaimed 5 1 3 7 4 No Information 4 6 9 3 3 . ± The 5 participants in the ³critically acclaimed´ condition are led to believe that these are paintings that are not famous but are highly thought of by a group of professional art critics. ± The 5 in the control condition are given no special information about the paintings.01 level of significance.

Linear models .

... n>2 y = a*x + b x = predictor y = predicted value (outcome) a = slope b= y-axes intercept Goal: determine parameters a.yi}.b .n. i=1.Review linear regression Simplest form Fit a straight line through data points {xi .

Review linear regression Find values for a and b such that sum of squared error is minimized .

Review linear regression Predicted values y*=ax+b Measurments y n minimize R ( a. b) ! §(y i !1 n i !1 * i yi ) 2 ! § ((axi b) yi ) 2 A minimum of a function (R) is characterized by a zero first derivative with respect to the parameters .

1) ! 2.Intermezzo: minimum of function dy ! 2x y!x dx dy min y ! 2x ! 0 dx x!0 2 dy x ! 1.1 ! 2 (1.2 dx dy x !0 ! 2 (0) ! 0 dx .

Review linear regression A minimum of a function (R) is characterized by a zero first derivative with respect to the parameters this provides the parameter values for the model function .

Review linear regression minimize (a. b) n ! § ( axi b yi ) ! 0 xb i !1 a Explicit expressions for parameters a and b!! . b) n ! § ( axi b yi )xi ! 0 xa i !1 x ( a. b) ! § ((axi b ) yi ) i !1 n 2 x ( a.

. ) Examples of linear models y= + x (linear) y= + x+ x2 (polynomial) y= + log(x) (log) .Linear and nonlinear models 1 (non) linear in the parameters ( .

Example: y ! 2 x ax 2 y varies linear with a for fixed x .

Example: y ! a log( x) y varies linear with a for fixed x .

Linear and nonlinear models 2 y= + 1x1 + 2x2 + -linear model (in parameters) -y is linear combination of x¶s 0 F1 2 y ! F 0 F 2 x2 x1 -y is not a linear combination of x¶s -linear in the parameters -We can use MLR if variables are transformed x1¶=1/x1 x2¶=x2 y = 0 + 1x1¶ + 2x2¶ + .

Linear and nonlinear models 3 Models like y!e F0 F1 x cannot be linearized and must be solved with nonlinear regression techniques .

Linear and nonlinear models 4 Nonlinear model: At least one of the derivatives of the function wrt the parameters depends on at least one of the parameters (thus. slope of line at fixed x is not constant) y ! e F0 F1x dy ! xe F0 F1x d F1 Nonlinear model y = log(x) dy/d = log(x) Linear model y = 0 + 1x1 + dy/d 1 = x1 Linear model 2x 2 .

Significance testing and multiple testing correction .

05 threshold.05? . Assume that all of the observations are explainable by the null hypothesis.Multiple testing Say that you perform a statistical test with a 0. but you repeat the test on twenty different observations. What is the chance that at least one of the observations will receive a p-value less than 0.

what is the chance that at least one of the observations will receive a p-value less than 0.358 Pr(making at least one mistake) = 1 .358 = 0.95 Pr(not making any mistake) = 0.0.05 Pr(not making a mistake) = 0.Multiple testing Say that you perform a statistical test with a 0. Assuming that all of the observations are explainable by the null hypothesis.2% chance of making at least one mistake.05 threshold.05? Pr(making a mistake) = 0. .9520 = 0.642 There is a 64. but you repeat the test on twenty different observations.

Percentage sugar in candy (process 1) Percentage sugar in candy (process 2) no difference statistical test (alpha=0. They are willing to accept an Type 1 error of 5%.05) 100 candy bars 100 candy bars 5% change of finding a difference Suppose the company is required to do an expensive tuning of process 2 if a difference is found. . Thus only 5% of making wrong decision.

05) statistical test (alpha=0.2% Day 20 statistical test (alpha=0.05) Change of 64.2% of finding at least one significant difference Overall Type 1 error = 64.05) .Percentage sugar in candy (process 1) Percentage sugar in candy (process 2) no difference Day 1 Day 2 statistical test (alpha=0.

For the previous example. Pr(making a mistake) = 0. 0.0. It is clear though that this highly increases the beta error (false negative).05 / 20 = 0.0025 Pr(not making a mistake) = 0.Bonferroni correction Assume that individual tests are independent. which is that many tests that should show an effect get below the corrected threshold.9512 = 0.0025.9512 Pr(making at least one mistake) = 1 . Divide the desired p-value threshold by the number of tests performed.0488 «meaning that the probability of one of the total number of tests being wrongfully said to be significantly different is of magnitude alpha (0.0488) This is also known as correcting for the Family Wise Error (FWE).997520 = 0. .9975 Pr(not making any mistake) = 0.

0025) Change of 4.88% Day 20 statistical test (alpha=0.88% of finding at least one significant difference Overall Type 1 error = 4.0025) .Percentage sugar in candy (process 1) Percentage sugar in candy (process 2) no difference Day 1 Day 2 statistical test (alpha=0.0025) statistical test (alpha=0.

2. Multiple comparison # of nonrejected hypotheses #Ho = true U # of rejected hypotheses V (false positives) m0 # Ho = false T (false negatives) S m1 m-R R ³discoveries´ m .

the proportion of false discoveries among the discoveries (0 if none found) FDR = E(Q) Does it make sense? .e.The False Discovery Rate (FDR) criterion Benjamini and Hochberg R = # rejected hypotheses = # discoveries of these may be in error = # false discoveries The error (type I) in the entire study is measured by V Q! R !0 R"0 R!0 i.

Does it make sense? Inspecting 100 features: 3 false ones among 60 discovered .bearable 3 false ones among 4 discovered .unbearable So this error rate is adaptive The same argument holds when inspecting 10.000 So this error rate is scalable .

Linear step up procedure (BH procedure. 0 2) . 0 k) If no such k exists reject none ... FDR procedure) Order the p-values P(1) P(2) « P(m) Let k ! ax{i:p(i) e(i / m)q} 0 1) Reject ..FDR controlling proceures..

0000008 0.00010 0.0000013 0.00035 0.0000235 0.0000056 0.00020 0. for all the genes above it.0000945 0.05 m=1000 Rank 1 2 3 4 5 6 7 8 9 10 « 1000 (j )/m 0. effective p-value threshold is 0.FDR example q=0.05000 p-value 0.0008900 1. (jq)/m is larger than the corresponding pvalue.00040 0.0000078 0. Thus.00050 0.0004700 0.00025 0.00030 0. Approximately 5% of the examples above the line are expected to be false positives.00015 0.0002450 .0002450 0.0000000 Choose the threshold so that.00005 0.0000012 0.00045 0.

The FDR is very different from a p-value. Meanwhile an FDR of as high as . and as such a much higher FDR can be tolerated than with a p-value.3 is generally unacceptabe in any circumstance. especially if there are thousands of genes on the array most of which are not differentially expressed. For example if the algorithm returns 100 genes with a false discovery rate of .5 or even higher might be quite meaningful. .3 then we should expect 70 of them to be correct. In contrast p-value of .FDR and p-value The False Discovery Rate (FDR) of a set of predictions is the expected percent of false predictions in the set of predictions. In the example above a set of 100 predictions of which 70 are correct might be very useful.

g. Use more flexible FDR procedures if certain proportions of false positives are tolerable (e. selecting candidate genes for RTPCR validation). Loss of power due to strong control of type-I error. 2.False discovery rate When to use FWER and when to use FDR? FWER=Pr(V>0)=Pr(at least one false positives) FDR=E(Q)=E(V/R) 1. gene discovery). Choose FWER if high confidence in ³ALL´ selected genes is desired (for example. .

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