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  • genArise: Easy R tool for microarray data analysis

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    genArise is an R package that contains functions for analyzing dual-color microarray data to detect differentially expressed genes under different growth conditions. It performs transformations on the data like background correction, normalization, and filtering to improve data quality before analysis. Key steps include calculating expression ratios (R) and intensities (I), normalizing data using loess regression to remove intensity-dependent biases, and identifying differentially expressed genes with a z-score approach comparing expression values to the mean and standard deviation.

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    GenArise Methodology

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    genArise is an R package that contains functions for analyzing dual-color microarray data to detect differentially expressed genes under different growth conditions. It performs transformations on the data like background correction, normalization, and filtering to improve data quality before analysis. Key steps include calculating expression ratios (R) and intensities (I), normalizing data using loess regression to remove intensity-dependent biases, and identifying differentially expressed genes with a z-score approach comparing expression values to the mean and standard deviation.

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    © All Rights Reserved
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    20 views2 pages

    genArise: Easy R tool for microarray data analysis

    Uploaded by

    Anonymous MqprQvjEK
    genArise is an R package that contains functions for analyzing dual-color microarray data to detect differentially expressed genes under different growth conditions. It performs transformations on the data like background correction, normalization, and filtering to improve data quality before analysis. Key steps include calculating expression ratios (R) and intensities (I), normalizing data using loess regression to remove intensity-dependent biases, and identifying differentially expressed genes with a z-score approach comparing expression values to the mean and standard deviation.

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    © All Rights Reserved
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    genArise

    genAriseisaneasytousetoolfordualcolormicroarraydataimplementedintheR
    language.genAriseisapackagethatcontainsspecificfunctionstoperformananalysisof
    cDNA microarrays data todetect genes that aresignificantly differentially expressed
    underdifferentgrowthconditions.

    Before this analysis, genArise carry out a number of transformations on the data to
    eliminatelowqualitymeasurementsandtoadjustthemeasuredintensitiestofacilitate
    comparisons.

    Backgroundcorrection
    Given the data set, a background correction can be performed. This is optional, but
    recommended. The default background correction action is to subtract the Cy3
    background intensity from the Cy3 foreground intensity and the Cy5 background
    intensityfromtheCy5foregroundintensityforeachspotinthemicroarray.

    RandIvalues
    Afterthis,thelogdifferentialexpressionratioandameasureoftheoverallbrightnessfor
    eachspotarecomputed.ThelogratioisrepresentedbytheR=log 2(Cy5)log2(Cy3),
    and the overall intensity by the I = log10(Cy5) + log10(Cy3). genArise use base2
    logarithmsforRsotheratioisunitsof2foldchange.

    Lowessnormalization
    genArisecancarryoutthenormalizationwithinthearray.TheimbalanceintheCy5and
    Cy3intensitiescanvarywidelyacrossthespotswithinthearray,andthisvariationcan
    beduetooverallspotintensity,locationonthearray,slideorigin,andpossiblyother
    variables.

    Duetospatialandintensitydependentbiasesinnumerousexperiments,genAriseusea
    localweightedregression(loess)analysis.Thisnormalizationmethodcanremovesuch
    intensitydependenteffectsinthelog2(ratio)values.

    Lowess,canbeappliedeitherglobally(overallthemicroarraydataset)orlocally(over
    each subgrid). We recommend to apply the local normalization, because it has the
    advantage that it can help correct for systematic spatial variation in the array, for
    example,inconsistenciesamongtheprinttips.
    Filterbyintensity
    With the purpose of eliminate those points where the intensity is to close to their
    correspondingbackground. Also,eachCy3valueinthespotmustbegreaterthantwo
    standarddeviationsfromCy3backgroundvalues,thesamecriterionforCy5.Inother
    way,theelementiseliminated.

    Replicatesanalysis
    Replicatesanalysisisareplicaaveragingfunction.Thisfunctionmergesthereplicated
    spotsbypresentingtheCy3intensitiesandCy5intensitiesasasingleaveragevalueof
    thereplica.

    ThreemethodshavebeenimplementedingenArisetoobtainthisaveragevalue.Thefirst
    ofthemisthearithmeticmeanofbothvalues,thesecondisthegeometricmeanand
    finallytheextremevalues(ifthelogratiooftheelementispositiveandthereplicatedis
    positivetoo,genArisekeepthemaximumofbothofthem,ifthelogratiooftheelement
    isnegativeandthereplicatedis negative, keeptheminimum,if bothofthemhave
    differentsign,theelementiseliminated).

    SelectingDifferentiallyExpressedGenes
    ThegoalofgenAriseistoidentifywhichofthegenesshowgoodevidenceofbeing
    differencially expressed. This function identify differential expressed genes by
    calculating an intensitydependent Zscore. We use a sliding window algorithm to
    calculatethemeanandstandarddeviationwithinawindowsurroundingeachdatapoint,
    anddefineaZscorewhereZmeasuresthenumberofstandarddeviationsadatapointis
    fromthemean.

    zi=(Rimean(R))/sd(R)

    whereziisthezscoreforeachelement,Riisthelogratioforeachelement,andsd(R)is
    thestandarddeviationofthelogratio.

    Withthiscriterion,theelementswitha|zscore|>2standarddeviationswouldbethe
    significantlydifferentiallyexpressedgenes.

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