[BioC] replace error reading 2color txt data into limma

[Gordon Smyth]

>Susan J. Miller sjmiller at email.arizona.edu
>Thu Oct 27 23:14:49 CEST 2005
>
>I am hoping someone can tell me what is causing this problem.  I am
>using R 2.1.0, limma 2.0.2 on a Windows 2000 system. I have four .txt
>files containing 2-color microarray data.  If I read each individual txt
>file it seems to work, but when I try to read all of the files I get the
>error shown below:
>
>[...]

By far the most likely explanation is that your files are of different 
lengths. To check this, read each data file into a separate object and 
check the size by dim(RG). I think you would also find it useful to use the 
'annotation' argument to read.maimages.

limma is only intended to read data files which correspond to the same set 
of probes in the same order, and you are expected to check this yourself. 
Note the following from help("read.maimages"):

Warnings:

      All image analysis files being read are assumed to contain data
      for the same genelist in the same order. No checking is done to
      confirm that this is true.


Gordon