Dear all, I have a conceptual problem with the "makeContrast" function in Limma: doing a factorial design and the follow are the targetfile and the design matrix targetfile FileName Scrofa Treatment S10M S127 DR S11 S52 DR S12 S304 DR S13 S9 NODR S14 S52 DR S15 S304 DR S17rt S304 DR S18 S66 DR S19 S66 NODR S20 S304 NODR S21 S93 NODR S22 S93 NODR > design S127.DR S304.DR S304.NODR S52.DR S66.DR S66.NODR S9.NODR S93.NODR 1 1 0 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 3 0 1 0 0 0 0 0 0 4 0 0 0 0 0 0 1 0 5 0 0 0 1 0 0 0 0 6 0 1 0 0 0 0 0 0 7 0 1 0 0 0 0 0 0 8 0 0 0 0 1 0 0 0 9 0 0 0 0 0 1 0 0 10 0 0 1 0 0 0 0 0 11 0 0 0 0 0 0 0 1 12 0 0 0 0 0 0 0 1 attr(,"assign") [1] 1 1 1 1 1 1 1 1 attr(,"contrasts") attr(,"contrasts")$TS [1] "contr.treatment" I want see the difference between the NODR and the DR group taking in account that they belong to different mothers ( S127 S304 .....etc ). How can I set the makeContrast.... I tried in this two ways.... but I don't know the difference between the first and the second 1)cont.matrix <- makeContrasts( DRvsNODR=(S127.DR+S304.DR+S52.DR)-(S30 4.NODR+S66.NODR+S9.NODR+S93.NODR), levels=design) 2) cont.matrix <- makeContrasts( DRvsNODR=(S127.DR-S304.DR-S52.DR)-(S3 04.NODR-S66.NODR-S9.NODR-S93.NODR), levels=design) Could you help me please??? Thanks in advance! Lorenzo

Hello Lorenzo, I am not sure if I understand your question correctly, but here is my $0.02. If you want to account for effect of mother, it would be better include it in your regression model as a factor, but I guess your aim is to detect the difference between DR and NODR (right?). If I understand you correctly (ie you are interested in NODR vs DR comparison), you probably want to model mothers as blocks. The duplicateCorrelation option in limma might come in handy in this case. Thanks, S. On Wed, Oct 6, 2010 at 12:56 PM, Lorenzo Bomba <lory.bomb@gmail.com> wrote: > Dear all, > > I have a conceptual problem with the "makeContrast" function in Limma: > doing a factorial design and the follow are the targetfile and the design > matrix > > targetfile > > FileName Scrofa Treatment > S10M S127 DR > S11 S52 DR > S12 S304 DR > S13 S9 NODR > S14 S52 DR > S15 S304 DR > S17rt S304 DR > S18 S66 DR > S19 S66 NODR > S20 S304 NODR > S21 S93 NODR > S22 S93 NODR > > > > design > S127.DR S304.DR S304.NODR S52.DR S66.DR S66.NODR S9.NODR S93.NODR > 1 1 0 0 0 0 0 0 0 > 2 0 0 0 1 0 0 0 0 > 3 0 1 0 0 0 0 0 0 > 4 0 0 0 0 0 0 1 0 > 5 0 0 0 1 0 0 0 0 > 6 0 1 0 0 0 0 0 0 > 7 0 1 0 0 0 0 0 0 > 8 0 0 0 0 1 0 0 0 > 9 0 0 0 0 0 1 0 0 > 10 0 0 1 0 0 0 0 0 > 11 0 0 0 0 0 0 0 1 > 12 0 0 0 0 0 0 0 1 > attr(,"assign") > [1] 1 1 1 1 1 1 1 1 > attr(,"contrasts") > attr(,"contrasts")$TS > [1] "contr.treatment" > > I want see the difference between the NODR and the DR group taking in > account that they belong to different mothers ( S127 S304 .....etc ). How > can I set the makeContrast.... > I tried in this two ways.... but I don't know the difference between the > first and the second > > 1)cont.matrix <- makeContrasts( > DRvsNODR=(S127.DR+S304.DR+S52.DR)-(S304.NODR+S66.NODR+S9.NODR+S93.NO DR), > levels=design) > > 2) cont.matrix <- makeContrasts( > DRvsNODR=(S127.DR-S304.DR-S52.DR)-S304.NODR-S66.NODR-S9.NODR-S93.NO DR), > levels=design) > > Could you help me please??? > > Thanks in advance! > > Lorenzo > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]