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Question: Affymetrix Human Exon Array MPS and PS files contain different probeset groups
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gravatar for Daniel Brewer
10.4 years ago by
Daniel Brewer1.8k
Daniel Brewer1.8k wrote:
This is not strictly a bioconductor question, but it is in the processing I use bioconductor and someone might have a similar experience. I use "apt-probeset-summarize" to produce Exon-level and gene-level signals. Different probesets are assigned to a gene or Exon based on the evidence to support this association. I use the "core" grouping. This grouping is defined by two files, one a probeset file (PS) which is simply a list of identifiers and the meta-probeset file which is a file with four columns: 1) probeset_id 2) transcript_cluster_id (Always same as 2) 3) probeset_list (list of probesets associated with the transcription cluster) 4) probe_count (the total number of probes) I might be confused about the true meaning of the meta probeset file but from what I can see, the probesets in a particular grouping should be in both the mps and the ps files if associated with a gene. This does not appear to be the case. For example if we look at the PTEN gene (3256689). The mps file (HuEx-1_0-st-v2.r2.dt1.hg18.core.mps) has the following line: 3256689 3256689 3256702 3256703 3256704 3256705 3256740 3256780 24 i.e. there are 6 probesets associated (3256702, 3256703,3256704, 3256705,3256740 & 3256780). Using NETAFFX or HuEx-1_0-st-v2.r2.dt1.hg18.core.ps+HuEx- 1_0-st-v2.na21.hg18.probeset.csv suggest that there are 23 core probesets associated with this gene ("3256702" "3256703","3256704","3256705","3256706", "3256707","3256708","3256709","3256710", "3256711","3256725","3256736","3256738", "3256739","3256740","3256764","3256767", "3256772","3256773","3256777","3256778", "3256779" & "3256780"). This difference could significantly effect the gene summary results. Does anyone know whether this discrepancy is on purpose? and if so way? Am I using the correct mps file? Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}
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