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

[James W. MacDonald]

Hi Yemi,

The p-value here is associated with the F-statistic, which is testing to 
see if *any* of your contrasts is significant. As I mentioned in my 
first response to your question, you probably want to look at the 'coef' 
argument of topTable,

     coef: column number or column name specifying which coefficient or
           contrast of the linear model is of interest. For 'topTable',
           can also be a vector of column subscripts, in which case the
           gene ranking is by F-statistic for that set of contrasts.

which seems pretty clear to me.

Best,

Jim


yemi yomi wrote:
>  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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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
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