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Hi Saurin, Saurin D. Jani wrote: > Hi BioC, > > For affymetrix microarrays, I have two groups: WT (wild type) and KO (knock out). I normalize data by some method, and then I do following steps for all my GeneChips. > > - Perform t-test > - generate p-value > - get Fold Change > - compute adjusted p-value (BH method) > > Now, I do filter genes based on two options, please let me know which is better. > > OptionsA: > - filter genes which satisfies p-value and fold change threshold and > get number genes and get max. adjusted p-value. as FDR. > > OptionsB: > - filter genes which satisfies BH-FDR (fdr x) and I get N number of genes, so, then I do Fold Change threshold so, I get N-1 genes and report N-1 genes with x fdr. > > is my x fdr is still true for N-1 genes or no? because have done extra step after I filter genes based on fdr. No, the fdr will not be accurate any more. Best, Jim > > Thank you so much in advance, > Saurin > > --------------------------------- > > [[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, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623