I have an experiment with 4 different conditions.
My idea was to use the contrast function to make the comparisons between the conditions but some comparisons don't seem to have have any DE genes.
Since this was disappointing I wanted to make sure I was using the contrast function properly so this time I only imported the data from 2 conditions instead of 4. And I compared
res <- results(dds) with
res2 <- results(dds, contrast=c("condition","A","B")).
Shouldn't the results from
res2 be the same in this situation? But they are not.
Thanks for your help.
head(res2)I was able to figure out that I made a mistake in the design matrix.
Now that I've fixed that the results of
res <- results(dds)and
res2 <- results(dds, contrast=c("condition","A","B"))match up.