Chi Square Analysis

Prepared by:
Sir Arnel Celestino
Can you tell what these pictures all about?
Yes, you are right. IT is…

Student: Eh, Sir, ano pong connect sa lesson lalo sa GENETICS?

Well, it is connected to our lesson on Chi Square Test. Unlike, those

examples (previous pictures), we can directly “JUDGE” the differences.
Even in genetics, probably in your future THESIS, the final outcome may
not be similar to your expected results. But, there still hope, because you
may use STATISTICAL TEST, whether the result is accepted or rejected.
Chi Square Test (χ2 test)
Introduction
• It is a widely used statistical test with the advantage of using any level
of variables such as nominal, ordinal, numerical or ratio.

• In Genetics, it is a simple way to quantify and illustrate the various

deviations from the expected outcomes of the alleles in a population.

• The assumption, like any statistical tests, is that there are no

significant deviations between the observed results and the predicted
outcomes.
Better picture: Null Hypothesis (Ho): Observed = Expected
• Chi square statistic formula is:

• where O is the observed number of cases, and E is the expected

number of cases, Ʃ is Summation
Example: Coin FLIP
• A coin can have a two probable outcomes, which are heads and tails.
• We can say that when we flip a coin, there is a 50% chance for a head
and 50% for tail as a result, thus, there will 50:50 or 1:1 ratio.
• As an example, I flipped a coin 100 times. I got a result of 54 heads
and 46 tails. We already know that there is 50:50 or 1:1 ratio as
possible outcome. We can say that the expected outcome should be
50 heads and 50 tails.

• So the Chi Square Statistic/Test, can answer the question:

Does my result (54 heads and 46 tails) is equal to the expected ratio?
Does my result (54 heads and 46 tails) deviated to the expected ratio?
Let us define first which is Observed and Expected,
then, simply substitute it in the formula given.

You can also use tables like this:

Observed Expected (O – E)2

E
Heads 54 50 0.32

Tails 46 50 0.32

Ʃ (O – E)2 0.64
E
 Student: Sir, Is that all?
• Not Yet, We just computed the Chi Square (χ2) value for that example

• We should also know the dF or degrees of freedom

*dF = n-1 ; where number of classes or categories

• We should compare it with the

Critical Values of the χ2 Distribution (Table)

• Commonly used significance level is 0.05 or 5%

• Accept the null hypothesis
• (O=E)

• Reject the null hypothesis

• (O≠E)
• From the example, there are only two outcomes (head or tail) so we
substitute 2 for n, then we can compute for dF
dF = n-1 ; dF = 2-1 ; dF = 1

• From the table, the critical value for dF=1 at 0.05 significance level is
3.84

• The calculated χ2 value is 0.64. Comparing it with 3.84, it is less than.

0.64 < 3.84, so the null hypothesis (1:1 ratio/ O=E) is accepted.

• We can now say that the result of flip coin with 54 Heads and 46 Tails
conform with the 1:1 ratio
Practice this Genetic Problem
• Mendel’s experiment on crossing pea flower with purple and white
produced all purple as F1. He again bred two F1 purple. He observed
733 purple flower pea plants and 267 white flower pea plants. With
our current knowledge of F2 phenotypic ratio of 3:1, does the
outcome of Mendel’s experiment coincides with the expected ratio?

• You can use pen and paper and ready your calculator.

• You can use the table format.

Expected: Total number X Probability Ratio
Purple : 1000 x (3/4) = 750
White : 1000 x (1/4) = 250
Phenotype Observed Expected (O – E)2
E
Purple 733 750 0.38533
White 267 250 1.156
Ʃ (O – E)2 1.541
E

*TRY TO ANSWER IT FIRST!

*ANSWERS are in White Color, to see Highlight the last column

• There are two phenotypes so the df = 1, let us use the 0.05
significance level so the critical value is 3.84

• Is the computed Chi square value lesser than or greater than 3.84

• If you got greater value, try to practice it again

• If you got lesser, you are correct! So we can say Mendel’s experiment
agree with the ratio of 3:1
For your Activity,

• Answer the Worksheet provided in Activity 3 Chi Square Analysis

References
• Gomez, K. A., & Gomez, A. A. (1984). Statistical procedures for
agricultural research. John Wiley & Sons.

• Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic

Analysis. 7th edition. New York: W. H. Freeman; 2000. Chi-square
test. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21907/

• https://bio.libretexts.org/Bookshelves/Biotechnology/Bio-
OER_(CUNY)/09%3A_Genetics/9.04%3A_Probability_and_Chi-
Square_Analysis