[BioC] limma fit interpretation doubt
David Moriña Soler
david.morina at uab.cat
Wed Feb 26 14:09:21 CET 2014
Dear Bioconductor users,
I just began to use limma package for the analysis of microarray data. I
want to include in the analysis two factors (treatment and time) and the
interaction between them. My design matrix looks like
> head(design)
Treat1.0h Treat1.6h Treat2.0h Treat2.6h
1 0 0 1 0
2 0 0 0 1
3 1 0 0 0
4 0 1 0 0
5 0 0 1 0
6 0 0 0 1
Then, if I run
> fit <-
lmFit(data.norm,design,block=pData(data)$Subject,correlation=corfit$consensus),
I have this output for the coefficients:
> head(fit$coefficients)
Treat1.0h Treat1.6h Treat2.0h Treat2.6h
KCNE4 5.020670 4.981786 5.038805 4.924326
IRG1 6.119265 6.015868 6.095171 6.027943
SNAR-G2 8.242385 8.186429 8.144942 8.230391
MBNL3 10.438644 10.417312 10.417042 10.358303
HOXC4 8.985834 8.854698 8.969801 8.939682
ENST00000319813 3.913602 4.102653 4.000681 3.960431
How can I obtain for example the effect of the treatment, using
contrasts and eBayes?
Thank you very much,
David
More information about the Bioconductor
mailing list