[BioC] Limma table results
Stefania [guest]
guest at bioconductor.org
Tue Apr 15 11:09:46 CEST 2014
Hi all,
I am using LIMMA package to analyse RNA-Seq data from a time course experiment. We have 3 time point, one control, two treatments and all the samples are in triplicate.
I used the spline method as suggested in the tutorial so I have:
yS<-DGEList(counts=limma.reads.counts)
SplineTargets=data.frame(File=sampleFileNames,Group=c(rep("Control",9),rep("Ofx",9),rep("MitC",9)),Time=c(rep(0,3),rep(30,3),rep(180,3),rep(0,3),rep(30,3),rep(180,3),rep(0,3),rep(30,3),rep(180,3)))
X <- ns(SplineTargets$Time, df=2)
Group <- factor(SplineTargets$Group)
spline.design <- model.matrix(~Group*X)
v <- voom(yS,spline.design,plot=FALSE)
fitSpline <- lmFit(v,spline.design)
fitSpline <- eBayes(fitSpline)
To extract the values of interest:
data.as.top.table = topTable(fitSpline,coef=6:9,n=500)
In the table result I have the columns
object..a.. GroupMitC.X1 GroupOfx.X1 GroupMitC.X2 GroupOfx.X2 AveExpr F P.Value adj.P.Val
Could you please help me in understanding the meaning of GroupMitC.X1, GroupOfx.X1, GroupMitC.X2, GroupOfx.X2 columns? How can I interpret this values? How are they associated with the behaviour of the gene?
Thanks in advance,
Stefania
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.0.1
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