[BioC] Filtering pmSequence based on probe target level for HTA 2.0 arrays

Steve Piccolo stephen.piccolo at hsc.utah.edu
Wed Aug 20 16:55:55 CEST 2014

List members,

I am working with some Affymetrix HTA 2.0 arrays. I have installed the
draft annotation package described here:

I am using the following commands from the oligo package to extract
intensity values and PM sequences via the oligo package. However, I am
running into a problem because the oligo::pmSequence function doesn't
allow me to specify a target probe type for these arrays. By default
oligo::pm() uses the "core" probes, whereas oligo::pmSequence only allows
me to use the "probeset" probes. In contrast, for the ST arrays, I am able
to do this.

affyExpressionFS <- read.celfiles(celFilePath)
pint = oligo::pm(affyExpressionFS, target="core")

pmSeq = oligo::pmSequence(affyExpressionFS, target="core")

Below is the error message I get.

Loading required package: pd.hta.2.0
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : testInputData/HTA2.CEL.gz
Error in { : task 1 failed - "unused argument (target = "probeset")"

Below is my session info. Any help would be appreciated.

R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
 [1] pd.hta.2.0_3.8.0    RSQLite_0.11.4      DBI_0.2-7
 [4] GEOquery_2.30.1     sva_3.10.0          mgcv_1.8-2
 [7] nlme_3.1-117        corpcor_1.6.6       foreach_1.4.2
[10] oligo_1.28.2        Biostrings_2.32.1   XVector_0.4.0
[13] IRanges_1.22.10     Biobase_2.24.0      oligoClasses_1.26.0
[16] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] affxparser_1.36.0     affyio_1.32.0         BiocInstaller_1.14.2
 [4] bit_1.1-12            codetools_0.2-8       compiler_3.1.0
 [7] ff_2.2-13             GenomeInfoDb_1.0.2    GenomicRanges_1.16.4
[10] grid_3.1.0            iterators_1.0.7       lattice_0.20-29
[13] Matrix_1.1-4          preprocessCore_1.26.1 RCurl_1.95-4.3
[16] splines_3.1.0         stats4_3.1.0          XML_3.98-1.1
[19] zlibbioc_1.10.0


Stephen Piccolo, Ph.D.
Postdoctoral Research Associate

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

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