Dear list and LIMMA users, I know this question is very often asked but I did not find the answer on the archives (and Limma user's guide, page 47). My experimental design is built as following : I have five replicates (human donors called 4 to 8 ) whom cells from blood were extracted and the same cells are treated (called DC) or not (called SC) for 4 hours and 18 hours. So, we can consider samples are paired. I only want the differential expressed genes between control and treated cells at 4 hours and 18 hours. Here is my code : > Treatment [1] DC DC DC DC DC SC SC SC SC SC DC DC DC DC DC SC SC SC SC SC Levels: DC SC > Time=factor(Targets$Time,level=c("4","18")) > Time [1] 4 4 4 4 4 4 4 4 4 4 18 18 18 18 18 18 18 18 18 18 Levels: 4 18 > Donor=factor(Targets[,4]) > Donor [1] 4 5 6 7 8 4 5 6 7 8 4 5 6 7 8 4 5 6 7 8 Levels: 4 5 6 7 8 > design=model.matrix(~0+Treatment*Time+Donor) > design > design TreatmentDC TreatmentSC Time18 Donor5 Donor6 Donor7 Donor8 TreatmentSC:Time18 1 1 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 0 3 1 0 0 0 1 0 0 0 4 1 0 0 0 0 1 0 0 5 1 0 0 0 0 0 1 0 6 0 1 0 0 0 0 0 0 7 0 1 0 1 0 0 0 0 8 0 1 0 0 1 0 0 0 9 0 1 0 0 0 1 0 0 10 0 1 0 0 0 0 1 0 11 1 0 1 0 0 0 0 0 12 1 0 1 1 0 0 0 0 13 1 0 1 0 1 0 0 0 14 1 0 1 0 0 1 0 0 15 1 0 1 0 0 0 1 0 16 0 1 1 0 0 0 0 1 17 0 1 1 1 0 0 0 1 18 0 1 1 0 1 0 0 1 19 0 1 1 0 0 1 0 1 20 0 1 1 0 0 0 1 1 attr(,"assign") [1] 1 1 2 3 3 3 3 4 attr(,"contrasts") attr(,"contrasts")$Treatment [1] "contr.treatment" attr(,"contrasts")$Time [1] "contr.treatment" attr(,"contrasts")$Donor [1] "contr.treatment" > fitDCSIGN = lmFit(DCSIGNsel,design) > fit_2<- eBayes(fitDCSIGN) > topTABLE=topTable(fit_2,number=10000) > head(topTABLE) TreatmentDC TreatmentSC Time18 Donor5 Donor6 Donor7 Donor8 TreatmentSC.Time18 AveExpr F P.Value adj.P.Val 18,0039565 18,0893776 -0,06921285 0,14003761 0,00751388 -0,17959668 -0,39518169 -0,05774869 17,9121781 9084,80254 3,28E-35 4,64E-31 17,6764306 17,6523265 0,10861812 0,08220318 -0,0058706 -0,12147117 -0,08119136 0,04533621 17,7047557 8639,31256 5,55E-35 4,64E-31 17,5451093 17,4890185 0,03333055 0,06786226 -0,03553932 -0,07273565 -0,13275773 0,08237079 17,5196878 8586,73092 5,92E-35 4,64E-31 17,5984155 17,5441874 0,10250253 0,01347935 -0,07462801 -0,35432923 -0,26347048 -0,06969421 17,4693395 7910,39319 1,39E-34 8,20E-31 17,665938 17,51601 0,12567687 0,10254981 0,0012268 -0,39209921 -0,44094147 0,13771659 17,5423888 7711,69463 1,82E-34 8,42E-31 17,4376721 17,5047189 0,06959671 0,07916199 -0,08220435 0,01004729 0,01116857 -0,06673615 17,4929445 7589,67631 2,15E-34 8,42E-31 17,3227449 17,3110054 0,05350864 0,07092431 0,01562233 -0,11608052 -0,22506562 0,03662242 17,3018652 7460,38367 2,57E-34 8,63E-31 So, I don't understand the colnames and why I did not obtain log fold change ? Is my design correct ? Many thans for your reply !!! Ingrid -- Ingrid MERCIER Mycobacterial Interactions with Host Cells Team Institute of Pharmacology& Structural Biology CNRS BP 64182 F-31077 Toulouse Cedex France Tel +33 (0)5 61 17 54 63 [[alternative HTML version deleted]]