[BioC] marray and gathering additional information from GenePix GPR file

Daniel Brewer daniel.brewer at icr.ac.uk
Fri Jul 7 12:32:27 CEST 2006


I am new to the use of bioconductor, so bear with me.  I am using
GenePix as my image processing software for cDNA arrays.  As it is set
up there is an automated procedure that determines whether a spot should
be considered for further use, and it uses the Normalize column to
indicate this (value of 1 accept, value of 0 drop).  I would like to
filter out all the "bad" spots after normalisation.

I use the following to read in the GPR files.
> mraw <- read.GenePix(targets=TargetInfo,name.Gb = NULL, name.Rb = NULL)

mraw at maW, successfully gives the flag values, but the Normalize column
does not appear to be in the object.  Is there anyway to input this

Many thanks

Daniel Brewer


Daniel Brewer, Ph.D.

Institute of Cancer Research

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