[BioC] how to select on Present calls in 2 out of 5 chips

James W. MacDonald jmacdon at med.umich.edu
Thu Oct 13 17:13:36 CEST 2005

Andreas Zankl wrote:
> I want to filter my expression data to accept only genes that have 
> the MAS5 "present" call in at least 2 out of 5 samples. How could I 
> do that? I know there are ALL and ANY commands in R, is there 
> something like a SOME or AT_LEAST command?

Easy enough to do without such a function. Say you have all the 
present/absent calls in a matrix called 'pcalls'.

index.calls <- pcalls == "Present"
index <- rowMeans(index.calls) =< 2

> Thanks
> Andreas

James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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