Can anyone tell me if the t-tests generated by the SimpelAffy pairwise.filter function which are applied to pairwise.comparison objects have been corrected for multiple testing? If so which correction is applied by default and are there any options? Regards, Dr. Brian Lane Northwest Institute for Bio-Health Informatics University of Liverpool

Brian Lane wrote: > Can anyone tell me if the t-tests generated by the SimpelAffy > pairwise.filter function which are applied to pairwise.comparison objects > have been corrected for multiple testing? If so which correction is applied > by default and are there any options? First, a pedantic note; neither the t-test nor the t-statistic are adjusted for multiplicity. The only statistic that is commonly adjusted is the p-value. However, it doesn't help that these functions use 'tt' to indicate the t-test p-value. I can see where you might have been lead astray. Anyway, if you dig through the functions, you will see that the p-values are not adjusted. They come from either fastT() in the genefilter package, or t.test() (for paired comparisons) in base R's stats package. HTH, Jim > > Regards, > Dr. Brian Lane > Northwest Institute for Bio-Health Informatics > University of Liverpool > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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