I am analyzing Affymetrix chips .

There are 8 chips, 4 relicates chips for treated and 4 for non-treated.
I used AffylmGUI and command line limma after rma(myData) normalization.
I would like to know upregulated genes in 'Treated' (group1 in the
following codes)
I think positive M values means upregulated in 'Treated' (group1), since
I did group1 - group2 'Treated' - 'non-treated'. Is it correct? Or
negative M value means upregulated in 'Treated'?

library(limma) 
library(affy)
data <- ReadAffy() 
eset <- rma(data) 
design <- model.matrix(~ -1+factor(c(1,1,1,1,2,2,2,2))) 
colnames(design) <- c("group1", "group2")
fit <- lmFit(eset, design) 
contrast.matrix <- makeContrasts(group1-group2, levels=design) 
fit2 <- contrasts.fit(fit, contrast.matrix) 
fit2 <- eBayes(fit2) 
topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10) 




Thank you.

Wonjong

> design
  group1 group2
1      1      0
2      1      0
3      1      0
4      1      0
5      0      1
6      0      1
7      0      1
8      0      1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$`factor(c(1, 1, 1, 1, 2, 2, 2, 2))`
[1] "contr.treatment"

> 


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