[BioC] read.maimages

[Jason Skelton]

Hi 

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


Cheers

Jason

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

   columns=list(Rf="Cy5",Gf="Cy3",Rb="Cy5.background",Gb="Cy3.background")

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
Hinxton
Cambridge
CB10 1SA

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