[BioC] Beadarray negative background values (bug?)

Richard Pearson richard.pearson at postgrad.manchester.ac.uk
Fri Sep 21 13:05:00 CEST 2007


For what its worth, I have seen this same problem myself when running 
beadarray on my mac. I didn't get the problem when running on linux.

Regards

Richard.


Arno Velds wrote:
> I'm seeing unexpected behavior using the beadarray package.
>
> When I'm doing the quantification from the TIFF files and the bead level 
> data files I'm seeing that almost half of the background values have a 
> very large negative value.
>
> I traced the problem into the c file (readBeadImages.c) that does the 
> background calculation. The background value is determined by taking the 
> 5 lowest pixel values from a 17x17 square from the centre of the bead. 
> The array containing those pixel values is initialized as M[289] which 
> is ok. However when you sort the array is calls: quicksort(M, 0, 289); 
> The third argument is used directly on the array and since arrays start 
> at index zero we possibly retrieve random memory.
>
> When I changed that call to  quicksort(M, 0, 288) no negative values are 
> calculated, but I think that doesn't solve everything: The R function 
> readIllumina takes an argument backgroundSize which allows you to 
> specify the background area. I set this value to 25 and the code 
> segfaults which makes sense since we fill the M array beyond the 288 limit.
>
> I think this is a bug, but if I misread the code somewhere feel free to 
> flame me :-) I also checked the dev version and saw no changes in the c 
> file so the problem is probably still there.
>
> Regards,
>
> Arno Velds
>
> The Netherlands Cancer Institute
> Amsterdam, The Netherlands
>
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