April 2016
Beginner to intermediate
1036 pages
33h 39m
English
book
Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition
by Sorin Draghici
Content preview from Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition
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Multiple comparisons 509
g19 -0.3025410 -0.04015468 0.26408682 1.268308841 -1.08545291
g20 1.6151907 0.45612104 0.13898369 2.168600317 0.57693730
> labels=c(rep("tumor",ncases),rep("control",ncases))
> mytest = function (x){
+ tumors = x[labels=="tumor"]
+ controls = x[labels=="control"]
+ p=t.test( tumors, controls,var.equal=TRUE)$p.value
+ foldchange=mean(tumors)-mean(controls)
+ c(foldchange,p)
+ }
> results=t(apply(data,1,mytest))
> rownames(results)<-rownames(data)
> colnames(results)<-c("logFC","p")
> results<-results[order(results[,2]),]
> results
logFC p
g17 -1.2425105 0.02109769
g15 -1.7077999 0.02664108
g8 0.8294332 0.05353653
g18 0.7093357 0.05961968
g13 -0.6270931 0.13584092
g16 1.0850587 0.13736632
g1 0.5179938 0.13742521
g14 0.9814332 0.16142621
g20 ...
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