[BioC] Duplicate probe coordinates with pd.hugene.2.1.st and oligo
Steve Piccolo
stephen.piccolo at hsc.utah.edu
Wed Jun 11 23:17:27 CEST 2014
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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