FAQ
Hello,

given the several requests I got re: supporting HTA 2.0 chips when using
oligo, I'm posting this message to bioc (rather than bioc-devel).

I'll add support for HTA on our next release. A draft is ready through the
devel branch. I may need to make some adjustments prior to the April
release.

For those interested in giving it a try, you'll need to have a developer
installation of Bioconductor (please, make sure to use a different path to
set your library and avoid mixing & matching). Then install oligo v.
1.27.3. With the devel bioc installed, you can use the usual:

biocLite('oligo')

You will also need an annotation package specific for HTA, which you can
download from here: (source version only)

https://dl.dropboxusercontent.com/u/83643/pd.hta.2.0_3.8.0.tar.gz

After downloading the annotation package, install it using:

## assuming that you loaded R from the directory where the
## package was downloaded to.
install.packages('pd.hta.2.0_3.8.0.tar.gz', repos=NULL)


Once both are installed, you should be able to run the standard:

library(oligo)
cels = list.celfiles()
raw = read.celfiles(cels)
pp0 = rma(raw, target='core')
pp1 = rma(raw, target='probeset')

to obtain your preprocessed data through oligo.

The annotation package will be made available through Bioconductor in the
next few weeks (devel branch again).

If you're in the mood of building your own annotation package, after
ensuring you have the aformentioned packages (and versions) installed, also
install pdInfoBuilder (version 1.27.4). Then, you can use the template
below to create your package:

## code to build HTA annot pkg
library(pdInfoBuilder)
seed <- new("AffyHTAPDInfoPkgSeed",
             version="3.8.0",
             license="Artistic-2.0",
             pgfFile=dir(patt=".pgf$"),
             clfFile=dir(patt=".clf$"),
             probeFile=dir(patt="probeset.csv$"),
             transFile=dir(patt="transcript.csv$"),
             coreMps=dir(patt=".mps$"),
             geneArray=TRUE,
             author="Benilton Carvalho",
             email="beniltoncarvalho@gmail.com",
             biocViews="AnnotationData",
             genomebuild="hg19",
             organism="Homo sapiens",
             species="Homo sapien",
             url="http://about.me/benilton")
makePdInfoPackage(seed, destDir=".")
## end

If you have any feedback/comment, please contact me.

benilton

Search Discussions

  • Mark Cowley at Feb 10, 2014 at 3:48 am
    thanks Benilton!


    On 09/02/2014, at 8:47 AM, Benilton Carvalho wrote:

    Hello,

    given the several requests I got re: supporting HTA 2.0 chips when using
    oligo, I'm posting this message to bioc (rather than bioc-devel).

    I'll add support for HTA on our next release. A draft is ready through the
    devel branch. I may need to make some adjustments prior to the April
    release.

    For those interested in giving it a try, you'll need to have a developer
    installation of Bioconductor (please, make sure to use a different path to
    set your library and avoid mixing & matching). Then install oligo v.
    1.27.3. With the devel bioc installed, you can use the usual:

    biocLite('oligo')

    You will also need an annotation package specific for HTA, which you can
    download from here: (source version only)

    https://dl.dropboxusercontent.com/u/83643/pd.hta.2.0_3.8.0.tar.gz

    After downloading the annotation package, install it using:

    ## assuming that you loaded R from the directory where the
    ## package was downloaded to.
    install.packages('pd.hta.2.0_3.8.0.tar.gz', repos=NULL)


    Once both are installed, you should be able to run the standard:

    library(oligo)
    cels = list.celfiles()
    raw = read.celfiles(cels)
    pp0 = rma(raw, target='core')
    pp1 = rma(raw, target='probeset')

    to obtain your preprocessed data through oligo.

    The annotation package will be made available through Bioconductor in the
    next few weeks (devel branch again).

    If you're in the mood of building your own annotation package, after
    ensuring you have the aformentioned packages (and versions) installed, also
    install pdInfoBuilder (version 1.27.4). Then, you can use the template
    below to create your package:

    ## code to build HTA annot pkg
    library(pdInfoBuilder)
    seed <- new("AffyHTAPDInfoPkgSeed",
    version="3.8.0",
    license="Artistic-2.0",
    pgfFile=dir(patt=".pgf$"),
    clfFile=dir(patt=".clf$"),
    probeFile=dir(patt="probeset.csv$"),
    transFile=dir(patt="transcript.csv$"),
    coreMps=dir(patt=".mps$"),
    geneArray=TRUE,
    author="Benilton Carvalho",
    email="beniltoncarvalho at gmail.com",
    biocViews="AnnotationData",
    genomebuild="hg19",
    organism="Homo sapiens",
    species="Homo sapien",
    url="http://about.me/benilton")
    makePdInfoPackage(seed, destDir=".")
    ## end

    If you have any feedback/comment, please contact me.

    benilton

    [[alternative HTML version deleted]]

    _______________________________________________
    Bioconductor mailing list
    Bioconductor at r-project.org
    https://stat.ethz.ch/mailman/listinfo/bioconductor
    Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
  • Elena Serrano at Apr 25, 2014 at 12:58 pm
    Hi!

    Thank you a lot Benilton! The package works very nicely! I have analyzed my
    first HTA2.0 arrays without any problem!

    Best regards,
    Elena


    2014-02-08 22:47 GMT+01:00 Benilton Carvalho <beniltoncarvalho@gmail.com>:
    Hello,

    given the several requests I got re: supporting HTA 2.0 chips when using
    oligo, I'm posting this message to bioc (rather than bioc-devel).

    I'll add support for HTA on our next release. A draft is ready through the
    devel branch. I may need to make some adjustments prior to the April
    release.

    For those interested in giving it a try, you'll need to have a developer
    installation of Bioconductor (please, make sure to use a different path to
    set your library and avoid mixing & matching). Then install oligo v.
    1.27.3. With the devel bioc installed, you can use the usual:

    biocLite('oligo')

    You will also need an annotation package specific for HTA, which you can
    download from here: (source version only)

    https://dl.dropboxusercontent.com/u/83643/pd.hta.2.0_3.8.0.tar.gz

    After downloading the annotation package, install it using:

    ## assuming that you loaded R from the directory where the
    ## package was downloaded to.
    install.packages('pd.hta.2.0_3.8.0.tar.gz', repos=NULL)


    Once both are installed, you should be able to run the standard:

    library(oligo)
    cels = list.celfiles()
    raw = read.celfiles(cels)
    pp0 = rma(raw, target='core')
    pp1 = rma(raw, target='probeset')

    to obtain your preprocessed data through oligo.

    The annotation package will be made available through Bioconductor in the
    next few weeks (devel branch again).

    If you're in the mood of building your own annotation package, after
    ensuring you have the aformentioned packages (and versions) installed, also
    install pdInfoBuilder (version 1.27.4). Then, you can use the template
    below to create your package:

    ## code to build HTA annot pkg
    library(pdInfoBuilder)
    seed <- new("AffyHTAPDInfoPkgSeed",
    version="3.8.0",
    license="Artistic-2.0",
    pgfFile=dir(patt=".pgf$"),
    clfFile=dir(patt=".clf$"),
    probeFile=dir(patt="probeset.csv$"),
    transFile=dir(patt="transcript.csv$"),
    coreMps=dir(patt=".mps$"),
    geneArray=TRUE,
    author="Benilton Carvalho",
    email="beniltoncarvalho@gmail.com",
    biocViews="AnnotationData",
    genomebuild="hg19",
    organism="Homo sapiens",
    species="Homo sapien",
    url="http://about.me/benilton")
    makePdInfoPackage(seed, destDir=".")
    ## end

    If you have any feedback/comment, please contact me.

    benilton

    [[alternative HTML version deleted]]

    _______________________________________________
    Bioconductor mailing list
    bioconductor@r-project.org
    https://stat.ethz.ch/mailman/listinfo/bioconductor
    Search the archives:
    http://news.gmane.org/gmane.science.biology.informatics.conductor

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postedFeb 8, '14 at 9:47p
activeApr 25, '14 at 12:58p
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