Draft support for HTA 2.0 with oligo
0
0
Entering edit mode
@elena-serrano-6353
Last seen 8.1 years ago
Spain
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 > [[alternative HTML version deleted]]
Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 849 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6