Modified getFidMetaProbesetCore to account for the fact that the HTA 2.0 arrays should use the transcript_cluster_id from the MPS file rather than meta_fsetid when summarizing at the core level. If we do not do this, there are 3000 probesets (including the ERCC probesets) that get annotated with the wrong probeset ID.
Merge pull request #21 from jmacdon/hta_fixes_JWM

Modified getFidMetaProbesetCore to account for the fact that the HTA 2.0...
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Commit information:

    Commit id: f3d36871680b8a3f2b8fd091bd26e5199c4b6e4f
    Commit message:
    Modified getFidMetaProbesetCore to account for the fact that the HTA 2.0 arrays should use the transcript_cluster_id from the MPS file rather than meta_fsetid when summarizing at the core level. If we do not do this, there are 3000 probesets (including the ERCC probesets) that get annotated with the wrong probeset ID.
    Committed by Jim MacDonald <jmacdon at ogopogo.deohs.washington.edu>
    Commit date: 2014-02-18T08:34:16-08:00

    Commit id: d6bb2141500027f03e85806779f8979bb0ca7154
    Commit message:
    Merge pull request #21 from jmacdon/hta_fixes_JWM

    Modified getFidMetaProbesetCore to account for the fact that the HTA 2.0...
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-02-18T16:24:45-08:00

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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@86565 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixing summarization for HTA chips
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    Commit id: 5cbf940324ce067db7ca507ca2c05841b871f12e
    Commit message:
    Fixing summarization for HTA chips
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-02-18T18:05:01-08:00

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modify to new biocViews to DESCRIPTION file



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
If phenoData is given, read.celfiles uses its sampleNames instead of using CEL filenames
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    Commit id: 3e3f0576d4b57012d87f9e2da0363258faa16348
    Commit message:
    If phenoData is given, read.celfiles uses its sampleNames instead of using CEL filenames
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-03-07T21:04:49-03:00

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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87218 bc3139a8-67e5-0310-9ffc-ced21a209358
Adding priority for sampleNames from phenoData to read.xysfiles
Merge branch 'master' of https://github.com/benilton/oligo
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Commit information:

    Commit id: 791d2a00b022d366083884fc80632c47516880db
    Commit message:
    Adding priority for sampleNames from phenoData to read.xysfiles
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-03-07T21:28:52-03:00

    Commit id: 5c5007fbc165bc1b7dc397d60e98f18f178c6cda
    Commit message:
    Merge branch 'master' of https://github.com/benilton/oligo
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-03-07T21:29:02-03:00

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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87222 bc3139a8-67e5-0310-9ffc-ced21a209358
Committing forgotten change
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    Commit id: 1cd41e04e6c9dff23a2650601301178db851b6c5
    Commit message:
    Committing forgotten change
    Committed by Benilton Carvalho <beniltoncarvalho at gmail.com>
    Commit date: 2014-03-10T15:13:01-03:00

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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo@87257 bc3139a8-67e5-0310-9ffc-ced21a209358
setting up git-svn bridge
Fixing date issue triggered by files without date/time info in header