Question: Draft support for HTA 2.0 with oligo
0
5.6 years ago by
Spain
Elena Serrano30 wrote:
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]]