[BioC] How extract F.p.value and lods values from a eBayes object in limma???

[Gordon Smyth]

>Date: Thu, 14 Apr 2005 15:07:56 -0300
>From: Marcelo Luiz de Laia <mlaia at fcav.unesp.br>
>Subject: [BioC] How extract F.p.value and lods values from a eBayes
>         object  in limma???
>To: bioconductor at stat.math.ethz.ch
>
>Hi,
>
>I do the commands:
>
>todos20050401.fit3 <- eBayes(todos20050401.fit2)
>selected <- p.adjust(todos20050401.fit3$F.p.value,method="fdr")<0.05
>selected.result <- todos20050401.fit3$genes[selected,]
>write.table(selected.result,"selected.F.p.value0.05.csv",sep=",")
>
>In my cvs file I get the name of genes, but I don t get the "F.p.value"
>nor "lods" values.

You've asked for the names of the genes with small values of F.p.value, and 
that's what you got.

>I try:
>
>todos20050401.fit3$genes[selected,],todos20050401.fit3$F.p.value,todos20050401.fit3$lods 
>
>
>Error: syntax error
>
>I read about cbind, but I don t obtain success, too.
>
>Please, Anyone point me if is possible todo?

The answer to the question in the title of your email is:

    todos20050401.fit3$F.p.value

and

    todos20050401.fit3$lods

What is it that you really want?

Gordon

>Thanks
>
>Marcelo