[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:

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,


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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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