I need some clarification on my results as i have been getting myself very confused!
I have an an microarray experiment where i have controls and cases (dosed with a drug). I have used the following in the design matrix for limma:
design <- model.matrix( ~CLASS) )
This creates a design matrix:
The zero's are my control group and the 1s are those samples dosed with the drug. Therefore the control group is my reference group.
From my output from limma for each gene i get a logFC. If i have a positive logFC for a gene does this mean that my gene is upregulated in my Drug group compared with my control group for that gene?
I have been reading lots of posts but i have now gotten very confused so any help will be appreciated!
Thanks for any help,