[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



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