Entering edit mode
Ido M. Tamir
▴
320
@ido-m-tamir-1268
Last seen 9.6 years ago
On Wednesday 30 November 2005 20:24, Guoneng Zhong wrote:
> Hi,
>
> Is there an easy way to merge data from a fit object (from lmFit)
and MA
> data (from normalizeWithinArrays) based on the genes? I mean, I
want
> the p values from the fit object and the different M values (each
column
> represents an original file), matching the data based on fit$gene or
> MA$gene.
>
> Basically, what I have now is:
> targets <- readTargets(targetFile)
> RG<-read.maimages(targets$FileName,columns=list(Rf="C5_Signal_Median
",Rb="C
>5_Signal_SD",Gf="C3_Signal_Median",Gb="C3_Signal_SD"),annotation=c('S
el_Crt'
>,'Probe_Seq','Feature_ID')) RG.noBG <-
backgroundCorrect(RG,method='none')
> MA.lnorm <- normalizeWithinArrays(RG.noBG, method="loess")
> design <- modelMatrix(targets,ref="Reference")
> fit<-lmFit(MA.lnorm,design)
> fit<-eBayes(fit)
>
I currently save tables of each of the contrasts together with the
original
values like this:
But I will (and you should) change a little bit
fit2Tables <- function(fit, expname, path, data ){
contrasts <- colnames(fit$lods)
for( ci in 1:length(contrasts)){
tt <- topTable( fit, coef=contrasts[ci], number=nrow(fit),
adjust.method="BH", sort.by="M" )
ttna <- topTable( fit, coef=contrasts[ci], number=nrow(fit),
adjust.method="none", sort.by="M" )
tt$p_unad <- ttna$P.Value
df <- data.frame( tt, data$M[as.integer(rownames(tt)),] )
colnames(df) <-
c(colnames(tt),paste(colnames(data$M),"M",sep="_"))
write.table( df, file=paste( path,"/", expname, "_",
contrasts[ci],
".tab", sep=""), sep="\t", row.names=FALSE, quote=FALSE )
}
}
change by untested:
tt$p_unad <- ttna$P.Value
to:
tt$p_unad <- ttna$P.Value[rownames(tt)]
just in case some probes have the same M values
Hope this helps
Ido
