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

[James W. MacDonald]

Hi Noah,

Noah Cohen wrote:
> 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.

I don't know if you would consider this more automated, but something like:

ttable <- topTable(fit)
ttable <- ttable[abs(ttable[,"M"] > 1,]

would do the trick.

Best,

Jim


> 
> 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
> 
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-- 
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


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