[BioC] question about topTable in limma

[Sean Davis]

On Mon, Apr 25, 2011 at 11:53 PM, samane fazeli <samanefazeli at gmail.com> wrote:
> Hello
>  Dear all
>  I have a question about topTable in limma package. Can i specify
> parameters of interest in
>  topTable, i.e. it gives me specific parameters such as adj.P-value
> and logFC, not ID and names
>  columns because both of them are caused to disorder output file of
> topTable. I would like to
>  process our data in excel
>
>  limma(library)
>  targets=readTargets("ApoAITargets.txt")
>  RG=read.maimages(targets$FileName, source="spot")
>  MA=normalizeWithinArrays(RG, method="loess")
>  controlRef=rep(1,16)
>  KOcontrol=c(rep(0,8),rep(1,8))
>  design=cbind(controlRef,KOcontrol)
>  fit=lmFit(MA,design)
>  fit=eBayes(fit)
>  option(digits=3)
>  result=topTable(fit, coef=2, number=6384, adjust="BH")
>  as.matrix(result)
>  write.csv(result,file="printtiploess.csv", quote=FALSE, col.names=TRUE,
>  sep=",")

Hi.  See the genelist argument to topTable().

Sean