I have multiple RNA-seq samples from 6 conditions and have to compare each condition against all the others: find genes dominant only in a specific group.
I tried two approaches.
First approach: separate all samples in 2 conditions: samples from one group vs samples from other groups, then repeat the operation 6 times switching the group against others.
Second approach: mark groups inside condition i.e.
Then run DESeq2 and perform final function with specific contrast. i.e
rds <- results(dds, contrast = list( c(g1),c(g2,g3,g4,g5,g6) ) )
In general, results were similar in both methods i.e. majority of the same genes were validated dominant using both approaches, however there were slight differences in lfcSE, p-values and q-values.
What is the most appropriate way to perform such analysis? Are there special settings to be applied for it? Is there a better method (i.e. ANOVA) to apply in this case?