Hi limma Users, I did a contrast in our analisis like this: (mutant treated-mutant control)-(wildtype treated-wildtype control) We are interested in to known what "M" value means in this situation? In limma users guide there are two interpretation for "M" value: fold change or intensities. Thanks in advanced Marcelo

Marcelo Luiz de Laia wrote: > Hi limma Users, > > I did a contrast in our analisis like this: > > (mutant treated-mutant control)-(wildtype treated-wildtype control) > > We are interested in to known what "M" value means in this situation? This contrast gives you those genes significant in the interaction. In other words, you are looking for genes that respond differently to treatment in the wild type samples as compared to the mutant. Therefore, the M value quantifies the fold change of the different responses. For instance, if gene x in the mutant sample is unaffected by treatment and the same gene in wildtype is downregulated two fold, the M value will be about 1 indicating that there is a two-fold difference in the response to treatment in the two groups. Does that help? Jim > > In limma users guide there are two interpretation for "M" value: fold > change or intensities. > > Thanks in advanced > > Marcelo > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Marcelo Luiz de Laia wrote: > Dear James W. MacDonald, > > I send directly to your mail box because I am not sure if this is > suitable for the maillist. You are free to correct me. It is suitable for the mail list, so I am responding there. I think there are enough people for whom English is a second language (depending on where you live, you may argue that this group includes the Americans ;-D) that a clarification might be enlightening. > > James W. MacDonald escreveu: > >> Marcelo Luiz de Laia wrote: >> >> >>> I did a contrast in our analisis like this: >>> >>> (mutant treated-mutant control)-(wildtype treated-wildtype control) >>> >>> >> >> In other words, you are looking for genes that respond differently to >> treatment in the wild type samples as compared to the mutant. >> >> > ops! A little confusion here, for me. > > In limma users guide (26/04/2005 p.36)I found: "Which genes respond > differently in the mutant relative to the wild-type? > >> cont.dif <- makeContrasts( > > + Dif6hr =(mu.6hr-mu.0hr)-(wt.6hr-wt.0hr), > + Dif24hr=(mu.24hr-mu.6hr)-(wt.24hr-wt.6hr),...)" > > Your advice frase above is oposite to limma users guide. Not? No, not really. The idea here is that we are looking for genes that react to treatment differently for one set of samples as compared to the other. Since microarrays are comparative assays, we are always comparing one set to the other. For instance, if a gene is unaffected in mutant samples when treated, but the expression goes down in wild type, then this gene responds differently in the mutant (no change) relative to the wild type (down-regulation). We can also say that this gene responds differently to treatment in the wild type samples (down-regulation) as compared to the mutant (no change). Therefore, both phrases have equivalent meanings. Does that help? Jim > > Thank you very much, again. > > Marcelo > > -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623