Question: Draft support for HTA 2.0 with oligo
0
5.6 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k 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@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]] ADD COMMENTlink modified 5.6 years ago by Mark Cowley910 • written 5.6 years ago by Benilton Carvalho4.3k Answer: Draft support for HTA 2.0 with oligo 0 5.6 years ago by Mark Cowley910 Mark Cowley910 wrote: 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 > > [[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