I am trying to produce a list of differentially expressed genes from microarray data from 7 different origins. I've compared the ouput of RP and RPadvance functions from the RankProd package and have noticed a smaller number of genes declared significantly differentially expressed at a pfp <= 0.05 in the output of RPadvance than RP. The package description says that supplying a vector of origins you affectively increase in statistical power, but I don't really understand how the rank product method works when considering different origins. If anyone can explain, this would be really helpful.
I am also curious as to why the genes found to be significantly up-regulated can also be found in Table2 (the list of genes significantly down-regulated? This just doesn't make any sense to me. Perhaps I am not understanding how RP and RPadvance work programmatically. Any help here would be great.