[BioC] Can Rank-production be applied to test the condition's effects on treatments?

[Kaj Chokeshaiusaha [guest]]

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


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