Hello, I'm new using LIMMA for the analysis of two color arrays. I have been following the user guide but I have questions regarding the meaning of the values and columns of the output "results" file. Where can I find an detailed explanation of the output file?, I mean the statistical definition of each column: A, Coef., t., p.value, F and Res. I guess that since I'm using adjust="fdr" in the code, the p values for each contrast are already adjusted for fdr and I can make my own cut (e.g. 5% or 1%) to find the MOST significant ones. Am I right?. Thanks, Andres Texas A&M University

Andres Gutierrez wrote: > Hello, > > I'm new using LIMMA for the analysis of two color arrays. I have been following > the user guide but I have questions regarding the meaning of the values and > columns of the output "results" file. > > Where can I find an detailed explanation of the output file?, I mean the > statistical definition of each column: A, Coef., t., p.value, F and Res. I guess > that since I'm using adjust="fdr" in the code, the p values for each contrast > are already adjusted for fdr and I can make my own cut (e.g. 5% or 1%) to find > the MOST significant ones. Am I right?. The output from topTable is already sorted with the genes most likely to be significant at the top, so you can set your cutoff to select genes with an FDR less than a certain level. As for a statistical definition, you might look at the Bioconductor Monograph. I thought the Limma User's Manual covered that pretty well too. Best, Jim > > Thanks, > > Andres > Texas A&M University > > _______________________________________________ > 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.

Dear Andreas, I am guessing that by a "results file" you mean the output from the write.fit() function. Sections 10.1 and 10.2 of the limma User's Guide give a detailed explanation of the columns from the topTable() function, and this pretty much explains everything from write.fit() as well. Yes, the p-values are FDR adjusted, although not the F.p.values. Yes, you can make your own cut. Best wishes Gordon > Date: Thu, 25 Jan 2007 16:25:28 -0500 > From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > Subject: Re: [BioC] Results file LIMMA > To: Andres Gutierrez <andresguty at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Message-ID: <45B92048.1070408 at med.umich.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > Andres Gutierrez wrote: >> Hello, >> >> I'm new using LIMMA for the analysis of two color arrays. I have been following >> the user guide but I have questions regarding the meaning of the values and >> columns of the output "results" file. >> >> Where can I find an detailed explanation of the output file?, I mean the >> statistical definition of each column: A, Coef., t., p.value, F and Res. I guess >> that since I'm using adjust="fdr" in the code, the p values for each contrast >> are already adjusted for fdr and I can make my own cut (e.g. 5% or 1%) to find >> the MOST significant ones. Am I right?. > > The output from topTable is already sorted with the genes most likely to > be significant at the top, so you can set your cutoff to select genes > with an FDR less than a certain level. > > As for a statistical definition, you might look at the Bioconductor > Monograph. I thought the Limma User's Manual covered that pretty well too. > > Best, > > Jim > > >> >> Thanks, >> >> Andres >> Texas A&M University >> >> _______________________________________________ >> 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