[BioC] EdgerR : paired analysis and block give different results

[anna [guest]]

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 

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