Hi,
in order to exclude any biased from socalled "SNP-in-probe" probes I want to mask certain probes when summarizing affymetrix probesets. I have a list of HuGeneST1.0 affymetrix probes I want to exclude (these are the 25pb-long probes, not the probesets).
I am using Affymetrix Power Tools (APT) using the following pseudo code:
apt-probeset-summarize -a rma-sketch --kill-list biasedProbes.txt *CEL
Where my biasedProbes.txt file looks like:
probeset_ID
440619
1025778
1080999
989305
425534
749434
648379
399148
896267
The error I am getting is:
FATAL ERROR:Probe kill list file, /home/simonlm/projects/PRAX/ExcludeSNPinProbe/data/biasedProbes.txt, does not have probeset_id column
Has anyone ever used APT in this form to exclude given probes? The error message makes me think I may not be able to exclude 25 bp probe-level, but only at the probeset level. Any ideas? Suggestions?
Thanks
1 answer
I got it to work. The file format APT expects is taken from HuGene-1_0-st-v1.hg19.probe.tab file, which can be downloaded from Affymetrix. Now my biasedProbes.txt file looks like this:
probe_id probeset_id x y assembly seqname start stop strand probe.sequence target.strandedness category
440619 7905533 668 419 build-GRCh37/hg19 chr1 152883670 152883694 + TCTGGGAGCTCCAGTTGCTTCTCCT Sense main
I believe columns 1:4 (probe_id, probeset_id, x, y) are sufficient.
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