Hi all, I have a question about the output from GOstats. What is the meaning Size column in the output of hyperGTest? e.g. GOBPID Pvalue OddsRatio ExpCount Count Size GO:0046599 0 -17.44695071 0.103006873 2 1 GO:0043006 0 -17.50880134 0.309020619 6 3 .... I thought Size is the number of elements belonging to the GO term in the specified universe, but it does not look to be so since the Count may be higher than Size. Second question: Is the hyperGTest returning the nominal Pvalues when used with a GOHyperGParams instance, or they are somehow adjusted? Thanks, Adi L. Tarca

Hi Adi, Tarca, Adi wrote: > Hi all, > I have a question about the output from GOstats. > What is the meaning Size column in the output of hyperGTest? > e.g. > GOBPID Pvalue OddsRatio ExpCount Count Size > GO:0046599 0 -17.44695071 0.103006873 2 1 > GO:0043006 0 -17.50880134 0.309020619 6 3 > .... > I thought Size is the number of elements belonging to the GO term in the > specified universe, but it does not look to be so since the Count may be > higher than Size. Second question: You are correct. It looks like you have a relatively old devel version of GOstats, as Seth fixed that bug months ago. Try updating and see if you get correct values. > Is the hyperGTest returning the nominal Pvalues when used with a > GOHyperGParams instance, or they are somehow adjusted? They are unadjusted p-values. Best, Jim > Thanks, > Adi L. Tarca > > _______________________________________________ > 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.