[BioC] Duplicate probe coordinates with pd.hugene.2.1.st and oligo

[Steve Piccolo]

I¹m trying to process some CEL files from Affy HuGene 2.1st platform. But
it seems there may be a problem with the pd.hugene.2.1.st package or with
the way oligo is handling them (or with something I am doing). Below is
the code that I am using and the output I¹m getting.

affyExpressionFS <- read.celfiles(celFilePath)
xCoord = getX(affyExpressionFS, type="pm")
yCoord = getY(affyExpressionFS, type="pm")

pmSeq = pmSequence(affyExpressionFS)

print(length(xCoord))
print(length(yCoord))
print(length(pmSeq))
print(length(shouldUseProbes))

[1] 1022045
[1] 1022045
[1] 1025088
[1] 1025088


Shouldn¹t the lengths of these all be identical? Also, I am seeing
duplicate values for the x_y coordinates. For example, it is saying there
are 8 probes with x_y coordinates of 1000_198, and the intensity values
are different for each probe.

Is there something I am missing? Or could this be due to a bug?



> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     

other attached packages:
 [1] SCAN.UPC_2.6.0      sva_3.10.0          mgcv_1.7-29
 [4] nlme_3.1-117        corpcor_1.6.6       foreach_1.4.2
 [7] affyio_1.32.0       affy_1.42.2         GEOquery_2.30.0
[10] oligo_1.28.2        Biostrings_2.32.0   XVector_0.4.0
[13] IRanges_1.22.8      oligoClasses_1.26.0 Biobase_2.24.0
[16] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] affxparser_1.36.0     BiocInstaller_1.14.2  bit_1.1-12
 [4] codetools_0.2-8       DBI_0.2-7             ff_2.2-13
 [7] GenomeInfoDb_1.0.2    GenomicRanges_1.16.3  grid_3.1.0
[10] iterators_1.0.7       lattice_0.20-29       MASS_7.3-33
[13] Matrix_1.1-3          preprocessCore_1.26.1 RCurl_1.95-4.1
[16] splines_3.1.0         stats4_3.1.0          tools_3.1.0
[19] XML_3.98-1.1          zlibbioc_1.10.0


Thanks,
-Steve

‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
Stephen Piccolo, Ph.D.
Postdoctoral Research Associate

Affiliations:
  Department of Pharmacology and Toxicology, University of Utah
  Division of Computational Biomedicine, Boston University School of
Medicine
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