Hello, when I analyse separately effects of treatment A or B in paired designs, each of them regulates significantly about 12000 tags, but when I analyse A and B together using a block design, I find that A regulates still 12000 tags, but B only 7000 tags, how come ? thanks, anna -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.