[BioC] What does the Pvalue column measures in LIMMA analysis

yemi yomi dejavuwide at yahoo.com
Tue Nov 11 15:03:08 CET 2008


 Dear All,

I carried out a time series analysis (4 time points with a common reference)  analysis of my dataset using LIMMA method. I set the design and contrast matrix as:
 
design<-model.matrix(~-1+factor(c(1,1,1,2,2,2,3,3,3,3,4,4,4,5,5,5,5,5)))
> colnames(design)<-c("E0.5Hrs","E0Hrs","E2Hrs","E4Hrs","WsHrs")
> fit<-lmFit(eset,design)
> contrast.matrix<-makeContrasts(E0Hrs-WsHrs,E0.5Hrs-WsHrs,E2Hrs-WsHrs,E4Hrs-WsHrs,levels=design)
> fit2<-contrasts.fit(fit,contrast.matrix)
> fit3<-eBayes(fit2)
> tab<-topTableF(fit3,adjust="fdr",n=14010)
the results from using topTableF give the following output example:
 
ID E0Hrs...WsHrs E0.5Hrs...WsHrs E2Hrs...WsHrs E4Hrs...WsHrs AveExpr F P.Value adj.P.Val
152598_at -0.310260187 0.799814391 2.450974615 1.029883808 9.976246414 47.14172706 3.31E-08 0.00043327
148500_at 0.09207473 0.12454068 0.681084397 -0.01071873 3.732942206 42.9457929 6.19E-08 0.00043327
147631_at 0.399408013 1.698760527 -0.067662327 -0.005311106 4.810342036 32.16015707 4.17E-07 0.001521181
154791_at 0.149794771 0.690132982 1.321826305 0.645885008 10.37671782 31.9551017 4.34E-07 0.001521181
 
I would appreciate it if anyone could explain what the Pvalue column is measuring? Or is there something wrong with my codes as I'm thinking of seeing separate pvalue columns for each contrasts set above.
 
Thanks
Yemi






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