[BioC] other.columns with ImaGene data (Limma read.maimages)

Gordon Smyth smyth at wehi.edu.au
Wed Jun 22 12:10:38 CEST 2005

>Date: Tue, 21 Jun 2005 16:51:40 +0100
>From: Richard Pearson <Richard.Pearson at postgrad.manchester.ac.uk>
>Subject: [BioC] other.columns with ImaGene data (Limma read.maimages)
>To: Richard Pearson <Richard.Pearson at postgrad.manchester.ac.uk>
>Cc: bioconductor at stat.math.ethz.ch
>I can't seem to get the other.columns to work in read.maimages. I have
>limma version 2.0.0. I have tried the following command:
>RG <- read.maimages(files, source="imagene"
>, other.columns=list(Col="Column",Row="Row",MetaCol="Meta
>Column",MetaRow="Meta Row",Flag="Flag")
>, wt.fun=mywtfun)
>This loads the intensity data fine but I have no "other" columns. I assume
>the problem is that this will call the read.imagene function which doesn't
>have an other.columns option - is this correct? Can anyone suggest a simple
>work around (my R is fairly limited at present!)?

You are correct that read.maimages() doesn't support 'other.columns' for 
ImaGene input. However you can use

f <- function(x) x$Flag
RG < read.maimages(files,source="imagene",wt.fun=f)

then RG$genes contains the columns "Column", "Row", "Meta Column" and "Meta 
Row" while RG$weights contains the flags.

Note also, if you use 'other.columns' for input from other sources, that 
this argument is a vector not a list.


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