[BioC] read.maimages

Jason Skelton jps at sanger.ac.uk
Tue Feb 3 12:04:19 MET 2004


I'm guessing the answer to my question is YES but are the Rb and Gb parts of read.maimages still compulsory ?
Or can I some how ignore them ?

I'm using some software (BlueFuse) that isn't supported by limma so I need to specify the column headers but the software
doesn't give background values just values for Cy3 & Cy5 as it's approach is different to other spot finding programs. 

So at the moment I'm having to make new columns for the background 
and give them values of 0 for each gene.

I've searched the mail achives and could only find this message from June 2003 
I was asking just in case anything has changed since then OR is there an option for making Rb & Gb NULL
or FALSE or something similar



Message: 4
Date: Thu, 19 Jun 2003 10:09:13 +1000
From: Gordon Smyth <smyth at wehi.edu.au>
Subject: Re: [BioC] read.maimages

The limma help documentation for 'read.maimages' says:

    columns: list with fields `Rf', `Gf', `Rb' and `Gb' giving the column
           names to be used for red and green foreground and background.

So you need something like


The names in double quotes are the column names in your file. The rest of 
the syntax is compulsory!

Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919

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