Affymetrix HuGeneST_1.0 masking probes

Question

[lkmklsmn]

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

Answer 1

[lkmklsmn]

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.