Hello, I'm using limma to normalize and analyse two colour dye swap arrays. In the output file I am getting two different p values: I. p.value II. F.p.value I attached an example of the command file I'm using. I suppose the first p value (p.value) is the raw p value and the second (F.p.value) is the p value adjusted with the FDR value. Can you please tell me if this assumption is correct and if it is correct to use this F.p.value to make conclusions on differential gene expression? Thank you very much, Stephanie Walter ================================== University College Dublin College of Life Sciences Belfield Dublin 4 Ireland -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: template commands CM 4h DON limma.txt Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060627/ d263345c/attachment.txt

Hi Stephanie, stephanie walter wrote: > Hello, > > I'm using limma to normalize and analyse two colour dye swap arrays. > In the output file I am getting two different p values: > I. p.value > II. F.p.value > I attached an example of the command file I'm using. > I suppose the first p value (p.value) is the raw p value and the > second (F.p.value) is the p value adjusted with the FDR value. Can you > please tell me if this assumption is correct and if it is correct to > use this F.p.value to make conclusions on differential gene > expression? No, you are not correct. The p.value is the p-value associated with a particular contrast, whereas the F.p.value is the p-value associated with the F-statistic which tests for a difference in _any_ of the factor levels. HTH, Jim > > Thank you very much, > Stephanie Walter > > > ================================== > University College Dublin > College of Life Sciences > Belfield > Dublin 4 > Ireland > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.