Odd Affymetrix Powertools Error For Human Exons St. 1.0 Data
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11.1 years ago
Paul ▴ 760

I'm trying to calculate which genes in my microarray samples are expressed above background (produce the dabg.summary.txt file). I've issued the following command in the linux terminal:

apt-probeset-summarize -a dabg -p supportFiles/HuEx-1_0-st-v2.r2.pgf -m  supportFiles/HuEx-1_0-st-v2.r2.dt1.hg18.core.mps -c supportFiles/HuEx-1_0-st-v2.r2.clf -b supportFiles/HuEx-1_0-st-v2.r2.genomic.bgp -o ./OUT_DABG_genomicBg *.CEL

Which gives the following strange error:

Processing Probesets............
FATAL ERROR:No background probes found for GC bin 24 for probe with id: 1025125
Perhaps there is no probe with GC count 24 in bgp-file: supportFiles/HuEx-1_0-st-v2.r2.genomic.bgp

The strange thing is when I use the antigenomic probeset file as background (HuEx-10-st-v2.r2.antigenomic.bgp) I get no error at all, but I need to use genonic (HuEx-10-st-v2.r2.genomic.bgp) to reproduce somebody else's results.

I've no idea what's going on here and found nothing online so any pointers would be a massive help.

Thanks!

affymetrix exon microarray • 2.3k views
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