I am trying to calculate differential gene expression between male and female samples. I successfully ran limma but the results somehow do not have negative values in the logFC column. I see the genes going up and down in both male and female sample, when I checked manually. But for some reason all the results have positive fold changes.
I thought maybe its because of my data design matrix?
Any comments would be appreciated.
data input file example
Male Female
gene1 2 10
gene2 30 3
gene3 4 5
gene5 0.4 4
How I created my design matrix
phenodata file
Name Gender
Male 1
Female 2
# limma
phenoData <-read.table("phenodata", head=T, row.names=1)
phenoData$Gender = as.factor(phenoData$Gender)
design <- model.matrix (phenoData$Gender, data=phenoData)
design
> design
phenoData$Gender
Male 1
Female 2
attr(,"assign")
[1] 1
> summary(decideTests(fit))
phenoData$Gender
-1 0
0 50944
1 19853