I am new to DE analysis, and I also looked for the answer to my question prior to writing, so sorry if there is a similar thread already and I couldn't find it.
I am trying to analyze the data from the RNA-seq analysis of the 5 different groups (A, B, C, D and E) with 3 biological replicates each. I would like to compare all my groups (B,C,D,E) to my control (A). My question now is: Is it better to compare the 2 specific groups at the time (B vs A, C vs A...) using the input raw counts file containing all the groups and replicates (e.g. A1, A2, A2, B1...) using the DESeq2 result function like this: res<- results(dds, name = "conditionBvs_A")?
Or, is it better to first create the file containing only the raw counts of A and B, and then perform DESeq analysis, using that input file only, and without specifying any 'name' in the result function, as following? res<- results(dds)
I tried both, and I obtained different numbers of DE genes.
I now don't understand why there is this difference (due to the different normalization possibly?), and which method is better to use?
Thank you, any help is appreciated. Snezana