Question: Affymetrix HTA 2 array analysis
0
5.8 years ago by
Spain
Elena Serrano30 wrote:
Hi all, Benilton, could you please update us if there is being some progress in getting the annotation files for HTA 2.0 affymetrix arrays? I am following this topic but I think there's not been any more comment after yours on 11/18/13 and I wonder whether I've missed something about the topic. Thank you in advance! Best regards, Elena Bioinformatician Scientific and Technical Platforms Biomedical Reseach Institute Sant Pau Santa Creu and Sant Pau Hospital Barcelona, Spain 2013/11/18 Benilton Carvalho <beniltoncarvalho@gmail.com> > Just very recently I got my hands on HTA CEL files, which give me the means > to assess other details that are needed for the annotation files. My > (internal) draft didn't work as planned, so rewriting a few things. Hope > to be able to get back to the maliling list soon. b > > > 2013/11/18 Stephen Turner <vustephen@gmail.com> > > > Just wondering if anyone has had any luck creating annotation packages > for > > the HTA 2.0 chip? > > > > Best, > > > > Stephen > > > > > > On Tue, Sep 10, 2013 at 8:24 PM, Mark Cowley <m.cowley@garvan.org.au> > > wrote: > > > > > Hi Vincent & Benilton, > > > Myself and Philip de Groot have independently tried to create the > > > pd.hta.2.0.db overnight with the same error (though different to your > > > error) on both R 2.15.2 on OSX and R 3.0.0 on linux. I probably should > > have > > > kept this on-list, so i'm CC'ing the relevant parties here. > > > Benilton, do you have any thoughts on what might be happening here? > > > > > > kind regards, > > > Mark > > > > > > > > > library(pdInfoBuilder) > > > baseDir <- getwd() > > > pgf <- "HTA-2_0.r1.pgf" > > > clf <- "HTA-2_0.r1.clf" > > > prob <- list.files(baseDir, pattern = ".probeset.csv",full.names=T)[1] > > > trans <- list.files(baseDir, pattern = > ".transcript.csv",full.names=T)[1] > > > mps <- list.files(baseDir, pattern = ".mps\$",full.names=T)[1] > > > seed <- new("AffyGenePDInfoPkgSeed", > > > pgfFile = pgf, clfFile = clf, > > > probeFile = prob, > > > coreMps=mps, author = "Mark Cowley", email="m.cowley@garvan.org.au > > > <mailto:m.cowley@garvan.org.au>", > > > biocViews = "AnnotationData",genomebuild = "NCBI Build 37", > > > organism = "Human", species = "Homo Sapiens", url = " > > > https://github.com/drmjc" > > > ) > > > makePdInfoPackage(seed, destDir = ".", unlink=TRUE) > > > > > > > > > ==================================================================== ============ > > > Building annotation package for Affymetrix Gene ST Array > > > PGF.........: HTA-2_0.r1.pgf > > > CLF.........: HTA-2_0.r1.clf > > > Probeset....: HTA-2_0.na33.hg19.probeset.csv > > > Transcript..: TheTranscriptFile > > > Core MPS....: HTA-2_0.r1.Psrs.mps > > > > > > > > > ==================================================================== ============ > > > Parsing file: HTA-2_0.r1.pgf... OK > > > Parsing file: HTA-2_0.r1.clf... OK > > > Creating initial table for probes... OK > > > Creating dictionaries... OK > > > Parsing file: HTA-2_0.na33.hg19.probeset.csv... OK > > > Parsing file: HTA-2_0.r1.Psrs.mps... OK > > > Creating package in ./pd.hta.2.0 > > > Inserting 850 rows into table chrom_dict... OK > > > Inserting 5 rows into table level_dict... OK > > > Inserting 11 rows into table type_dict... OK > > > Inserting 577432 rows into table core_mps... OK > > > Inserting 1839617 rows into table featureSet... Error in > > > sqliteExecStatement(con, statement, bind.data) : > > > RS-DBI driver: (RS_SQLite_exec: could not execute: datatype mismatch) > > > > > > # OSX > > > > sessionInfo() > > > # R version 2.15.1 (2012-06-22) > > > # Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > # > > > # locale: > > > # [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > > # > > > # attached base packages: > > > # [1] stats graphics grDevices datasets utils methods base > > > # > > > # other attached packages: > > > # [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 > > > # [4] affxparser_1.30.2 RSQLite_0.11.2 DBI_0.2-5 > > > # [7] Biobase_2.18.0 BiocGenerics_0.4.0 > > > # > > > # loaded via a namespace (and not attached): > > > # [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.3 > > > # [4] bit_1.1-10 codetools_0.2-8 ff_2.2-11 > > > # [7] foreach_1.4.0 GenomicRanges_1.10.7 IRanges_1.16.6 > > > # [10] iterators_1.0.6 parallel_2.15.1 > preprocessCore_1.20.0 > > > # [13] splines_2.15.1 stats4_2.15.1 zlibbioc_1.4.0 > > > > > > # linux > > > > sessionInfo() > > > R version 3.0.0 (2013-04-03) > > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > > > locale: > > > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > > > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > > > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > > > [7] LC_PAPER=C LC_NAME=C > > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > > > > > attached base packages: > > > [1] parallel stats graphics grDevices utils datasets methods > > > [8] base > > > > > > other attached packages: > > > [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 > > > [4] affxparser_1.32.1 RSQLite_0.11.4 DBI_0.2-7 > > > [7] Biobase_2.20.1 BiocGenerics_0.6.0 BiocInstaller_1.10.2 > > > > > > loaded via a namespace (and not attached): > > > [1] affyio_1.28.0 Biostrings_2.28.0 bit_1.1-10 > > > [4] codetools_0.2-8 ff_2.2-11 foreach_1.4.1 > > > [7] GenomicRanges_1.12.3 IRanges_1.18.1 iterators_1.0.6 > > > [10] preprocessCore_1.22.0 splines_3.0.0 stats4_3.0.0 > > > [13] tools_3.0.0 zlibbioc_1.6.0 > > > > > > > > > On 11/09/2013, at 1:44 AM, Vincent Carey <stvjc@channing.harvard.edu> > > <mailto:stvjc@channing.harvard.edu>> > > > wrote: > > > > > > We have obtained a large number of "glue grant array" cel files that > are > > > predecessors > > > of HTA 2.0. An informal attempt to process with the gene ST interface > in > > > pdInfoBuilder failed. We'd > > > be interested to hear of progress on the HTA 2.0 front. > > > > > > > > > > > > ==================================================================== ============ > > > Building annotation package for Affymetrix Gene ST Array > > > PGF.........: hGlue_3_0_v3.pgf > > > CLF.........: hGlue_3_0_v3.clf > > > Probeset....: hGlue_3_0_v1_Lib_v3.hg18.probeset.csv > > > Transcript..: TheTranscriptFile > > > Core MPS....: coreMps > > > > > > > > > ==================================================================== ============ > > > Parsing file: hGlue_3_0_v3.pgf... OK > > > Parsing file: hGlue_3_0_v3.clf... OK > > > Creating initial table for probes... OK > > > Creating dictionaries... OK > > > Parsing file: hGlue_3_0_v1_Lib_v3.hg18.probeset.csv... OK > > > Error in [.data.frame(probesets, , cols) : undefined columns selected > > > > > > [sessionInfo was not forwarded to me.... but more details can be > provided > > > if there is any interest] > > > > > > On Tue, Sep 10, 2013 at 2:45 AM, Mark Cowley <m.cowley@garvan.org.au> > > <mailto:m.cowley@garvan.org.au>> wrote: > > > Hi Steven, > > > Did you manage to create a pd.hta.2.0 package? > > > > > > kind regards, > > > Mark > > > > > > On 20/04/2013, at 7:23 AM, Steven McKinney <smckinney@bccrc.ca<mailto:> > > smckinney@bccrc.ca>> wrote: > > > > > > > Hi all, > > > > > > > > Has anyone developed bioconductor/R analysis tools for the > > > > Affymetrix Human Transcriptome Array HTA_2_0 ? > > > > > > > > Any information on processing data from this chip type > > > > would be appreciated. > > > > > > > > > > > > Best > > > > > > > > Steven McKinney > > > > > > > > Statistician > > > > Molecular Oncology and Breast Cancer Program > > > > British Columbia Cancer Research Centre > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org<mailto: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]] > > > > > > _______________________________________________ > > > 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]] > > > > _______________________________________________ > > 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]] > > _______________________________________________ > 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]]