[BioC] limma: topTable

[Julia Engelmann]

Sorry, here comes my code:

library(affy)
library(limma)
library(vsn)
data  	<- ReadAffy()
normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")
Set		<- expresso(data, normalize.method="vsn", 
bgcorrect.method="none",pmcorrect.method="pmonly", 
summary.method="medianpolish")

# R and T stand for different treatment, R1 and R2 as well as T1 and T2 are 
biological reps.
design      <- model.matrix(~ -1+factor(c(1,1,2,2,3,3,4,4))) 
colnames(design) <- c("R1","R2","T1","T2")
fit              <- lmFit(Set, design)
contrast.matrix  <- makeContrasts(((R1+R2)-(T1
+T2))/2,R1-T1,R2-T2,levels=design);
fit2             <- contrasts.fit(fit, contrast.matrix)
fit2             <- eBayes(fit2)
data          <- read.table("ATH1-121501_annot.csv", header=TRUE, sep=",")
res              <- topTable(fit2, number=10,coef=1, 
adjust="fdr",genelist=data,sort.by="P",resort.by="M")

Thanks a lot again,
Julia

> >Hi Bioconductor folks,
> >
> >I have really been enjoying using the limma package, but I have just come
> >across a problem.
> >When I use the topTable-command, the slot "result$Probe.Set.ID" does not
> > seem to match the other entries I am interested in, namely M, P, t.
> >I am using R 1.8.0, limma 1.5.5 on Affymetrix ATH1-121501 chips.
> >
> >An example would be:
> >Output of the topTable-result:
> >
> >                 Probe.Set.ID            M               t
> > P.Value         B
> >5598    259302_at       4.593339 38.9793 1.126260e-05 11.88238
> >
> >If I check on gene number 5598 it says
> >geneNames(myExprSet)[5598]
> >[1] "250498_at"
> >
> >Am I misinterpreting 5598 as the index of my ExpressionSet?
>
> I think you've done something non-standard, anyway you can't have simply
> used lmFit() and eBayes() and topTable() on our exprSet object. Please show
> us enough of your code so that we can see how topTable is getting the probe
> set ID's.
>
> Gordon
>
> >Thanks a lot for any suggestions!
> >Julia