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

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@mail.med.upenn.edu] Sent: Tuesday, August 10, 2004 11:27 AM To: bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor