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Arno Velds
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10
@arno-velds-2387
Last seen 10.3 years ago
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
