[BioC] Draft support for HTA 2.0 with oligo

[Mark Cowley]

thanks Benilton!

On 09/02/2014, at 8:47 AM, Benilton Carvalho <beniltoncarvalho at gmail.com>
 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
> 
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> 
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