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

[J.delasHeras at ed.ac.uk]

Quoting Daniel Brewer <daniel.brewer at icr.ac.uk>:

> Hi,
>
> 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
> information?
>
> Many thanks
>
> Daniel Brewer
>
> **************************************************************
>
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research

Hi Daniel,

You could try reading the gpr file with 'read.table' as a data frame, 
take the column you want from it, add it to your marray object and 
delete the data frame.

I don't use marray, I use limma, and I use the same procedure to import 
other columns I am interested in (in my case the SNR columns at the end 
of the gpr file, and perhaps the flags).

I hope it helps.

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
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