I use Ranprod to meta-analyze qPCR data from 3 studies (13 genes in total). Some of these genes are differentially expressed in the same direction (down-regulated) in the 3 studies with p<0.05 in the 3 studies. So I was expected Rankprod to classify them in the same group. In fact it does not. Some of these genes appears to be regulated in the other direction (up) which does not make sense to me. Does anybody have any idea why? Thanks for ay suggestion or some help? -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RankProd_2.26.0 loaded via a namespace (and not attached): [1] tools_2.14.1 -- Sent via the guest posting facility at bioconductor.org.