[BioC] Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder

Guilherme Rocha gvrocha at gmail.com
Tue Aug 26 16:00:36 CEST 2014

  Hi all,

  I have constructed a package information file for Affy's HTA 2.0 chip
using pdInfoBuilder as shown below.
  It appears that the annotation files have been upgraded to na34 (from
na33 in probeFile and transFile).

  Specific question: do the annotation files affect which probes are
included in each probeset/trascript cluster?
  Broader question: what information from the annotation files is actually
used by pdInfoBuider?

  Any help appreciated.


  Guilherme Rocha

Construction fo the package:



seed <- new("AffyHTAPDInfoPkgSeed",
            version     = "3.8.0",
            license     = "Artistic-2.0",
            pgfFile     = ".../HTA-2_0.r1.pgf",
            clfFile     = ".../HTA-2_0.r1.clf",
            probeFile   = ".../HTA-2_0.na33.hg19.probeset.csv",
            transFile   = ".../HTA-2_0.na33.1.hg19.transcript.csv",
            coreMps     = ".../HTA-2_0.r1.Psrs.mps",
            geneArray   = TRUE,
            author      = "gvrocha",
            email       = "gvrocha at gmail.com",
            biocViews   = "AnnotationData",
            genomebuild = "hg19",
            organism    = "Homo sapiens",
            species     = "Homo sapien",
            url         = "http://about.me/gvrocha")

makePdInfoPackage(seed, destDir=".")

Guilherme V. Rocha
gvrocha at gmail.com

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