[BioC] Is it possible to "filter" genes in topTable on basis of M values?

[Noah Cohen]

Hi – I am very much inexperienced and inexpert in use of BioConductor for analysis of cDNA microarray data.  With the help of the listserve (primarily Dr. Gordon Smyth), I have been able to learn to use limma for analysis of data from an equine leukocyte cDNA microarray developed by some friends at the University of Georgia.  I have fit a linear model to data from 12 microarray slides, each slide representing hybridization of cDNA from 1 of 12 horses with laminitis against cDNA from a reference sample (pooled cDNA from a group of healthy control horses).  

When I use topTable to try to identify which genes are differentially expressed, the number with an adjusted P value < 0.05 is quite long (several hundred genes).  I’d like to be able to filter the list in various ways; for example, excluding genes whose absolute value of M is < 1.  I know that I can do this manually by using the “sort.by” and “resort.by” options in topTable, but am looking for an alternative solution that is more automated.  Thanks for any help that can be provided.  

Noah Cohen


Noah D. Cohen, VMD, MPH, PhD, DACVIM
Professor
Department of Large Animal Clinical Sciences
College of Veterinary Medicine and Biomedical Sciences
Texas A&M University
College Station, Texas 77843-4475
Telephone: 979-845-3541
Fax: 979-847-8863
e-mail: ncohen at cvm.tamu.edu