[BioC] beadarray - readBeadLevelData problems

[Mark Dunning]

Hi Felix,

I looked at the files you sent me, and it seems you are trying to read a 
pgm image file into the package. This was the file format that was first 
used in readBeadLevelData, but we recently changed it to accept tif images 
instead (ie the images that come straight off the scanner). Try reading the 
tifs and see if that works.

Hope this helps,

Mark

PS we are currently making some changes to the package which will make the 
reading of bead level data easier and more efficient. The changes will 
shortly be submitted to the development version of the package.




On Feb 12 2007, Engel Felix wrote:

>Dear Mark,
> 
> we would like to use beadarray for analysis for bead level data analysis. 
> I use version 1.2.2 of your package and R 2.4.1 on Linux. The problem I 
> encounter while reading raw image data is that the function 
> readBeadLevelData does return an array with the correct probe position 
> information, but only zeros for the greenIntensities (as returned from 
> your external C function). Still, the function returns without error.
> 
>The location for the test files I use:
> 
>http://www.dkfz.de/genetics/supplement/engel/beadarray/beadarray.zip
> 
>Maybe you can offer some help.
> 
>Thank you so much.
> 
>Best regards,
> 
>Felix
>

-- 
Mark Dunning
Computational Biology Group
Department of Oncology, University of Cambridge / Cancer Research UK
Cancer Research Institute, Li Ka Shing Centre
Robinson Way
Cambridge CB2 0RE
UNITED KINGDOM
Tel: +44 1223 404295