hi, I have generated a list of significant genes for 3 time points separately using the function "decideTests"in Limma package.Using this function I generated foldchanges and FDR for every gene using method Benjamini and Hochberg ("BH") and p.value=0.05. I was wondering if it is possible to generate all the FDR and foldchanges with the respective gene name for every time point. I tried changing the cut-off to 1 in order not to exclude anything and the method set to the function "decideTests" changed to "none" but it doesn't work. Could you recommend any other possible ways? I would appreciate any help, Daphne

Hi Daphne, perhaps ?write.fit does what you want. Best Giovanni On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function > "decideTests"in Limma package.Using this function I generated > foldchanges and FDR for every > gene using method Benjamini and Hochberg ("BH") and p.value=0.05. > I was wondering if it is possible to generate all the FDR and > foldchanges with the respective > gene name for every time point. > I tried changing the cut-off to 1 in order not to exclude anything and > the method set to the > function "decideTests" changed to "none" but it doesn't work. > Could you recommend any other possible ways? > > I would appreciate any help, > > Daphne > > _______________________________________________ > 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

daphne mouzaki (RI) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function > "decideTests"in Limma package.Using this function I generated > foldchanges and FDR for every > gene using method Benjamini and Hochberg ("BH") and p.value=0.05. > I was wondering if it is possible to generate all the FDR and > foldchanges with the respective > gene name for every time point. If you want everything then decideTests() is probably not the function you want. Instead, you should try topTable(). Something like this should work: topTable(<marraylm object="">, coef = 1, number = <number of="" genes="" on="" chip="">) You can then change 'coef' to 2, 3,... depending on the number of contrasts you have. HTH, Jim > I tried changing the cut-off to 1 in order not to exclude anything and > the method set to the > function "decideTests" changed to "none" but it doesn't work. > Could you recommend any other possible ways? > > I would appreciate any help, > > Daphne > > _______________________________________________ > 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.