[BioC] @maControls in Read.Genepix

[Paquet, Agnes]

Dear Inma,

read.GenePix is using the function maGenControls to fill the maControls
field in your layout. To determine if a probe is a control, read.Genepix is
comparing each probe id to a look-up matrix named controlCode.

controlCode is a matrix with 2 columns named: Pattern and Name. You can
check the default controlCode by typing in R:
library(marray)
controlCode

There are several ways to specify your own controls. You could read your
controls in using the read.marrayLayout function in marray, or you can do
the following:

1. Build your own controlCode matrix and replace the existing one.
This can be done by either using the readcontrolCode function in marray or
by reading a tab-delimited text file directly.

controlCode <- as.matrix(read.table("mycontrolCode.txt",
sep="\t",header=TRUE, quote="\"", fill=TRUE)))


2. Define your controls in your marrayRaw object:
maControls(myObject) <- maGenControls(maGnames(myObject))

Best,

Agnes

-----Original Message-----
From: M Inmaculada Barrasa [mailto:ibarrasa at mail.med.upenn.edu] 
Sent: Tuesday, August 10, 2004 11:27 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] @maControls in Read.Genepix 



Hi Everyone,

Where can I find information on how "read.Genepix" is loading a gpr file.
In particular I would like to find out from which columns is it loading
the information for "@maControls". And how can I specify which are my
controls probes.

Thanks a lot for your help,

Inma




-- 
Inmaculada Barrasa Ph.D.
Research Associate
Department of Cancer Biology
Abramson Family Cancer Research Institute
320 BRB II/III
421 Curie Boulevard
University of Pennsylvania
Philadelphia, PA 19104

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