Dear R helpers, I'm studying the effects of different conditions on the same treatment. Similar to the following example, Condition A --- Control(Ca)(4 samples) VS Treatment(Ta)(4 samples) Condition B --- Control(Cb)(3 samples) VS Treatment(Tb)(4 samples) The control and treatment procedures in both conditions are the same, and I want to test the effects of conditions on treatment result, the differentially expressed genes acquired from (Ta-Ca) VS (Tb-Cb) with FDR<0.05 Would you please clarify me if it is possible to use RankProd for such question? Thank you very much in advances for your kind suggestions. With Respects, Kaj -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RankProd_2.36.0 loaded via a namespace (and not attached): [1] tools_3.1.0 -- Sent via the guest posting facility at bioconductor.org.