>[BioC] A limma question. >Johan Lindberg johlin at kth.se >Fri Apr 21 16:56:06 CEST 2006 > >I think this is kind of a stupid question but I cant get it right so >I will risk my hide. > ># First I do a topTable as usual, but without adjustment for multiple testing. >topt.dc <- >topTable(fit=ebobj,number=length(ebobj$coef),adjust.method="none",sor t.by="t") > > > topt.dc[1:3,] > M A t P.Value B >20861 -1.025634 -1.0256342 -14.87215 1.285609e-10 13.716847 >680 -1.889194 -1.8891945 -14.58354 1.711049e-10 13.493043 >24876 -1.861192 -1.8611920 -14.30543 2.264364e-10 13.271669 > ># The degrees of freedom for the moderated t-test is if I am not mistaken >df.dc <- ebobj$df.prior + ebobj$df.residual > ># If you look at the toptable the P-value for the first gene is 1.285609e-10 >and the t-value is -14.87215. > ># but if I try to get the t-value from the p-value by >qt(p=topt.dc[1,4], df=df.dc[idx.vec[1]],lower.tail = TRUE) >-14.18081 > >#which differs from -14.87215. The difference is bigger for the second gene. ># -13.9039 vs -14.58354 > >What am I doing wrong? You've forgotten that the p-values are two-sided. Best wishes Gordon >Best regards >// Johan Lindberg > >********************************************************************* ******* >Johan Lindberg >Royal Institute of Technology >AlbaNova University Center >Stockholm Center for Physics, Astronomy and Biotechnology >School of Molecular Biotechnology >Department of Gene Technology >Visiting address: >Roslagstullsbacken 21, Floor 3 >106 91 Stockholm, Sweden >Delivering address: >Roslagstullsbacken 30B >104 06 Stockholm, Sweden >Phone (office) +46 8 553 783 44 >Fax + 46 8 553 784 81 > <http: www.ktharray.se=""/> http://www.ktharray.se/ > <http: www.arrayadvice.se=""/> http://www.arrayadvice.se/ >********************************************************************* *******