Respected Madam/Sir,
I would like to know about contrasts matrixx between wild and mutant type
with replicates. Below you can see two
contrasts matrix and both have different results in term of + & - value like
*7.122005 & **-7.122005 *respectivily.
*
c<-makeContrasts(group2-group1,levels=design) **
*  topTable(fit2, coef=1, adjust="fdr", number=10)
               ID     logFC  AveExpr         t      P.Value
adj.P.Val         B
8516    253416_at  *7.122005* 7.535481  26.57534 2.255100e-05 0.3000238
1.4319777
21394   266294_at  *5.221736* 7.090044  24.38216 3.100325e-05 0.3000238
1.3731773

*OR **c<-makeContrasts(group1-group2,levels=design)

*topTable(fit3, coef=1, adjust="fdr", number=10)
               ID     logFC  AveExpr         t      P.Value
adj.P.Val         B
8516    253416_at *-7.122005* 7.535481 -26.57534 2.255100e-05 0.3000238
1.4319777
21394   266294_at* -5.221736* 7.090044 -24.38216 3.100325e-05 0.3000238
1.3731773

Could you telll me which one is correct ? because on the basis of these
value i select up/down expression ?

Thanks
Varpall

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