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
>
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>
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