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

[Claire Wilson]

Or alternatively you can use rowSums (assuming x contains your matrix of
PMA calls):
calls.sum <- rowSums(x=="P")
keep <- names(calls.sum[calls.sum>=2])

It's a little faster!

claire

-- 
Claire Wilson 
Bioinformatics Group 
Paterson Institute for Cancer Research 
Christie Hospital NHS Trust 
Wilmslow Road 
Manchester  
M20 4BX 
tel: +44 (0)161 446 8218  
url: http://bioinf.picr.man.ac.uk/bioinf/cwilson.jsp 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Crispin
Miller
Sent: 13 October 2005 16:59
To: Andreas Zankl
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] how to select on Present calls in 2 out of 5 chips

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

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
 
--------------------------------------------------------

 
This email is confidential and intended solely for the use\ ...{{dropped}}