>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!)? > >Regards > >Richard 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. Gordon