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

[Felix Engel]

Dear Mark,

I built the package myself, because the decimal separator is different 
in our Illumina data files (see code attached). I will not accept any 
Illumina software background correction. I am using gcc version 4.1.2 
with "-fpic  -march=pentium4 -O3 -pipe -std=gnu99"

Here my sessionInfo:

R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu

locale:
C

attached base packages:
[1] "grid"      "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
    beadarray beadarraySNP  quantsmooth      lodplot     quantreg 
SparseM
      "1.5.3"      "1.2.0"      "1.0.0"        "1.1"       "4.05" 
"0.72"
         affy       affyio  geneplotter      lattice     annotate 
Biobase
     "1.14.0"      "1.2.0"     "1.14.0"     "0.15-4"     "1.14.1" 
"1.14.0"
        limma
     "2.10.4"


Thanks,

Felix.

Mark Dunning wrote:
> 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.
> 
> Regards,
> 
> Mark
> 
> 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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> 
> 
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