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carol white wrote: > Hi, I have fitted a univariate cox regression a data set and retained > the genes whose p-value were less or equal to 0.05. the total number > of retained genes is 2746. I also filtered genes based on the same > condition (pval <= 0.05) on the same data set using coxfilter > function in genefilter package and got 2648 genes, i.e 98 genes less > than the number of genes that I got by univariate cox model. Should I > have not got the same number of genes? Not necessarily. It depends on what p-value you are using. The coxfilter function uses the likelihood ratio to compute a p-value. If you are using a Wald or Score test, the p-value may be different enough for some genes that they would pass your p-value filter, but not for the p-value returned from coxfilter. > > Moreover, I think the output of coxfilter is just a set of genes > whose pval <= a threshold like 0.05 and it doesn't provide a gene set > based on p-val ranking (ascending or descending) which I need. You are correct - coxfilter is designed to give TRUE/FALSE indices to filter your genes.. However, it wouldn't take much to change coxfilter to simply return the p-values (or alternatively for you to emulate coxfilter with your own function that will do what you want). Best, Jim > > regards, carol > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ 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.