[BioC] beadarray - raw data import - bead background intensities faulty

Mark Dunning md392 at cam.ac.uk
Thu Jun 14 09:29:16 CEST 2007

Hi Felix,

Could you tell me more about the system you are running please? If  
you run the function sessionInfo() it will say which version of the  
package you are using, the version of R and operating system. Did you  
download a compiled version of the package or did you build it from  
the source code on your own machine? I suspect that this is a C  
compiler issue, but  I need more information to be sure.



PS if you set useImages = FALSE in readIllumina, it will read the  
background corrected values found in the text files and skip the  
image processing steps. This will speed up the process of reading the  
raw data (if you are willing to accept what Illumina do for  
background correction!).

On 13 Jun 2007, at 16:00, Felix Engel wrote:

> Dear Mark Dunning.
> With the latest SVN version of beadarray the background-read problem
> (raw data import) remains, when issuing:
> BLData = readIllumina(imageManipulation = "none",
> backgroundMethod="none", textType=".txt")
> I still cannot explain resulting background values below zero:  
> There are
> 500000 beads with average intensity -215359277, where another 500000
> beads on the array give a normal background (average intensity 630).
> Thanks for your insight,
> Felix.
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