[BioC] Limma and Quantarray files

[Gavin Kelly]

> Hi,
> 
> I've a problem using limma with quantarray output files. I've changed
all output files to ANSI format,
> because the original Unicode format is not accepted by limma.
> I'm able to use one file per time without any trouble but when I try
to load more than
> one file using a "target" file using,
> 
>
>target<-readTargets(file="targets.txt",path="C:\\Playground\\CrossTest"
)
> 
>
>RG<-read.maimages(target,source="quantarray",path="C:\\Playground\\Cros
sTest")
> 
> I receive an error message like:
> 
> Read C:\Playground\CrossTest/PA52-Export.txt
> Error in if (skip > 0) readLines(file, skip) :
>         argument is of length zero
> 
> How can I solve this problem?
> 
> Kind Regards
> 
> Alessio
> 

Alessio,
I had a similar problem in a recent version of limma (not sure which
version you're using).  If you edit the source for read.maimages, and
look for the second instance of the line:

skip <- grep("Begin Data", firstfield)

and comment this out.  Save this as your own function, and it should
work okay.  This will only work if all your quantarray files have the
data (as flagged by the "Begin Data" string) starting at the same line.
If this is not the case, then you'll need to find the instance of the
phrase "nlines=100" just above the skip assignment, and remove
it/customise it to your files (and uncomment the skip assignment)

Hope this helps - Gavin

-- 
Gavin Kelly (DPhil) Senior Statistician
Bioinformatics & Biostatistics, Room 708
Cancer Research UK
44 Lincoln's Inn Fields
London WC2A 3PX
United Kingdom