I have a loop design experiment in which I compare two types of males and females. There are 6 individuals in each group. For the pairwise comparison I build the contrasts with the following: design_NT1 <- modelMatrix(targets, ref = "NT1") contrasts <- makeContrasts (NvsT = (NT2+NT3+NT4+NT5+NT6-T1-T2-T3-T4-T5-T6)/6, FvsN = (F1+F2+F3+F4+F5+F6-NT2-NT3-NT4-NT5-NT6)/6, TvsF = (T1+T2+T3+T4+T5+T6-F1-F2-F3-F4-F5-F6)/6, levels = design_NT1) Now i want to extract the difference between all males (regardless of type) and females, but I'm not sure how to do this? Thanks Suzy

Thanks for getting back to me Mark. Actually, I have 12 males and 6 females because there are two different male phenotypes, T and NT. So I had used: design_NT1 <- modelMatrix(targets, ref = "NT1") MvsF = (T1+T2+T3+T4+T5+T6+NT2+NT3+NT4+NT5+NT6-F1-F2-F3-F4-F5-F6)/6 but the number of significantly regulated genes that I got was a lot less than what I expected given the results that I get for TvsF and NTvsF. I to know what genes are upregulated in all males relative to females and thought that I could increase my statistical power by considering MvsF rather than just taking the intersection of the two gene lists that I got for TvsF and NTvsF. Is that wrong? Thanks Suzy Mark Cowley wrote: > Hi Suzy, > You have to know which of the labels are from males, or females. > I'll assume that (a) you have a balanced design and (b) all of the > even numbers are males, and odd numbers are females, and (c) NT1 is > the reference, then you'll need to specify a contrast like this: > MvsF=(T2+T4+T6+F2+F4+F6+NT2+NT4+NT6-T1-T3-T5-F1-F3-F5-NT3-NT5)/9 > cheers, > Mark > > On 25/07/2008, at 5:11 AM, renns wrote: > >> I have a loop design experiment in which I compare two types of males >> and females. There are 6 individuals in each group. For the pairwise >> comparison I build the contrasts with the following: >> >> design_NT1 <- modelMatrix(targets, ref = "NT1") >> contrasts <- makeContrasts (NvsT = >> (NT2+NT3+NT4+NT5+NT6-T1-T2-T3-T4-T5-T6)/6, FvsN = >> (F1+F2+F3+F4+F5+F6-NT2-NT3-NT4-NT5-NT6)/6, TvsF = >> (T1+T2+T3+T4+T5+T6-F1-F2-F3-F4-F5-F6)/6, levels = design_NT1) >> >> Now i want to extract the difference between all males (regardless of >> type) and females, but I'm not sure how to do this? >> >> Thanks >> Suzy >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > ----------------------------------------------------- > Mark Cowley, BSc (Bioinformatics)(Hons) > > Peter Wills Bioinformatics Centre > Garvan Institute of Medical Research, Sydney, Australia > ----------------------------------------------------- > >