this is output of limma ## ID logFC AveExpr t P.Value adj.P.Val B ## 9491 39400_at -0.9997850 5.634004 -5.727329 1.482860e-05 0.1034544 2.4458354 > eset["39400_at",] CLL11 CLL12 CLL14 CLL15 CLL16 CLL17 CLL18 CLL19 CLL20 CLL21 5.146120 6.494292 4.912334 4.927824 5.665698 6.190625 6.843152 5.408045 6.556617 5.148195 CLL22 CLL23 CLL24 CLL2 CLL3 CLL4 CLL5 CLL6 CLL7 CLL8 6.102306 4.776241 5.534030 6.538251 5.333660 5.364452 5.815452 5.422736 4.671384 5.698590 CLL9 5.764070 we can see :AveExpr =sum(eset["39400_at",])/21; but when i calculate the logFC, it is not -0.9997850 SampleID Disease 2 CLL11 progres. 3 CLL12 stable 5 CLL14 progres. 6 CLL15 progres. 7 CLL16 progres. 8 CLL17 stable 9 CLL18 stable 10 CLL19 progres. 12 CLL20 stable 13 CLL21 progres. 14 CLL22 stable 15 CLL23 progres. 16 CLL24 stable 17 CLL2 stable 18 CLL3 progres. 19 CLL4 progres. 20 CLL5 progres. 21 CLL6 progres. 22 CLL7 progres. 23 CLL8 progres. 24 CLL9 stable that is the process: sum_stable=eset["39400_at",][2]+eset["39400_at",][6]+eset["39400_at",] [7]+eset["39400_at",][9]+eset["39400_at",][11]+eset["39400_at",][13]+e set["39400_at",][14]+eset["39400_at",][21]> sum=sum(eset["39400_at",]) > sum=sum(eset["39400_at",]) > sum_prog=sum-sum_stable > ave_prog=sum_prog/13 > ave_stable=sum_stable/8 > fc=ave_prog/ave_stable log2(fc) -0.2513515 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

If your data is already log transformed then the logFC (log of fold change not fold change of the logs) is computed as ave_prog - ave_stable. I believe this is what limma does. On Mon, Sep 9, 2013 at 11:13 PM, Wang Peter <wng.peter@gmail.com> wrote: > this is output of limma > > ## ID logFC > AveExpr t P.Value adj.P.Val > B > > ## 9491 39400_at -0.9997850 5.634004 > -5.727329 1.482860e-05 0.1034544 2.4458354 > > eset["39400_at",] > CLL11 CLL12 CLL14 CLL15 CLL16 CLL17 CLL18 CLL19 > CLL20 CLL21 > 5.146120 6.494292 4.912334 4.927824 5.665698 6.190625 6.843152 5.408045 > 6.556617 5.148195 > CLL22 CLL23 CLL24 CLL2 CLL3 CLL4 CLL5 CLL6 > CLL7 CLL8 > 6.102306 4.776241 5.534030 6.538251 5.333660 5.364452 5.815452 5.422736 > 4.671384 5.698590 > CLL9 > 5.764070 > > we can see :AveExpr =sum(eset["39400_at",])/21; > but when i calculate the logFC, it is not -0.9997850 > > > SampleID Disease > 2 CLL11 progres. > 3 CLL12 stable > 5 CLL14 progres. > 6 CLL15 progres. > 7 CLL16 progres. > 8 CLL17 stable > 9 CLL18 stable > 10 CLL19 progres. > 12 CLL20 stable > 13 CLL21 progres. > 14 CLL22 stable > 15 CLL23 progres. > 16 CLL24 stable > 17 CLL2 stable > 18 CLL3 progres. > 19 CLL4 progres. > 20 CLL5 progres. > 21 CLL6 progres. > 22 CLL7 progres. > 23 CLL8 progres. > 24 CLL9 stable > > > that is the process: > > > sum_stable=eset["39400_at",][2]+eset["39400_at",][6]+eset["39400_at" ,][7]+eset["39400_at",][9]+eset["39400_at",][11]+eset["39400_at",][13] +eset["39400_at",][14]+eset["39400_at",][21]> > sum=sum(eset["39400_at",]) > > > sum=sum(eset["39400_at",]) > > sum_prog=sum-sum_stable > > > ave_prog=sum_prog/13 > > ave_stable=sum_stable/8 > > fc=ave_prog/ave_stable > > log2(fc) > > -0.2513515 > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839@cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]