[BioC] problem reading genepix files using both marray andlimma functions

[Bela Tiwari]

Hello,

Thanks for the responses about my email and the offers of help.

I have now upgraded to the latest version of limma from the wehi site. 
I also wrote to the person who provided the gpr files I have, and she
says they have not been touched/edited, etc. She copied new versions of
the files for me from a CD she burned when she first received the files,
and these are identical to the ones I have been using. (Same sizes, same
errors.)

I tried to load all the gpr files as before, using read.maimages. This
caused problems again, though the error message may be a bit more
telling this time perhaps (see below). 

I then tried loading just those files that  I had been able to load
individually without errors using the older version of read.maimages. -
this worked! Hurrah!  At least that's now a total of 8 of my files (of a
total of 16) that I can now load without problem.

Here is the error message that appeared when attempting to load all
files:

> mynewLimmaData <-read.maimages(gprfiles, source = "genepix")
Read A12797013.gpr
Error in "[<-"(`*tmp*`, , i, value = as.integer(c(53, 46, 49, 227, 57, 
:
        number of items to replace is not a multiple of replacement
length

Given this, I hope you don't mind if I take up your offer and end you a
couple of the gpr files (offlist). I hope you can spot the errors that I
am missing.  

I should, of course, have remembered to find out what version of limma I
was already using before I upgraded....oh well. I am pretty sure (from
another machine like mine), that this is the correct version info for
both R and limma:
>version
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    9.0
year     2004
month    04
day      12
language R



> packageDescription("limma")
Package: limma
Version: 1.6.7
Date: 2004/05/14
Title: Linear Models for Microarray Data
Author: Gordon Smyth <smyth at wehi.edu.au>, Matt Ritchie
        <mritchie at wehi.edu.au>, James Wettenhall
        <wettenhall at wehi.edu.au>, Natalie Thorne <thorne at wehi.edu.au>
Maintainer: Gordon Smyth <smyth at wehi.edu.au>
Depends: R (>= 1.7.1), MASS, splines, statmod (>= 1.0.6), sma
Description: Data analysis, linear models and differential expression
        for microarray data.
License: LGPL
URL: http://bioinf.wehi.edu.au/limma/
Packaged: Wed May 26 14:31:46 2004; madman
Built: R 1.9.0; ; 2004-07-27 16:54:06; unix
 

cheers,

Bela


*************************
Dr. Bela Tiwari
Lead Bioinformatician

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975