Dear list,
 
Is it possible to extract the group means + SD from Limma's output?
 
I do know that the "Amean" can be extracted (fit2$Amean), but this is
the mean across all arrays/groups, and i am also interested in the means
of the experimental groups.
Therefore, is it somehow possible to extact the mean (+ SD) of the
groups that are defined by the contrast matrix? Thus in my particular
case the mean + SD of the WT.Con, WT.WY. KO.Con and KO.WY groups.
 
Thanks,
Guido
 
 
library(affy)
library(limma)
 
targets <- readTargets("targets.txt")
data <- ReadAffy(filenames=targets$FileName)
x.norm <- rma(data)

TS <- paste(targets$Strain, targets$Treatment, sep=".") 
TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY"))
design <- model.matrix(~0+TS)
colnames(design) <- levels(TS)
fit <- lmFit(eset, design)
cont.matrix <- makeContrasts(WTwyvWTc=WT.WY-WT.Con,
KOwyvKOc=KO.WY-KO.Con, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



	[[alternative HTML version deleted]]

