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

[Crispin Miller]

Hi,
Have a look at the pairwise.comparison and pairwise.filter methods in
simpleaffy. Alternatively, you could try something like (assuming x
contains your matrix of PMA calls):

x[x=="P"] <- 1
x[x!=1]   <- 0

sums <- apply(x,1,sum)
keep <- (sums >= 2)

crispin

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Andreas
Zankl
Sent: 13 October 2005 16:01
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] how to select on Present calls in 2 out of 5 chips

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?

Thanks
Andreas

--
PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM

--------------------------
Andreas Zankl, MD
Division of Molecular Pediatrics
Clinique Infantile 02/50
CHUV
Avenue Pierre Decker 2
CH-1011 Lausanne
Switzerland
Phone: +41-21-3143778
Fax: +41-21-3143546
Email: andreas.zankl at gmail.com

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