Question: Affymetrix HTA 2 array analysis
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gravatar for Mark Cowley
6.0 years ago by
Mark Cowley910
Mark Cowley910 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 at="" 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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ADD COMMENTlink modified 6.0 years ago by Vincent J. Carey, Jr.6.3k • written 6.0 years ago by Mark Cowley910
Answer: Affymetrix HTA 2 array analysis
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gravatar for Vincent J. Carey, Jr.
6.0 years ago by
United States
Vincent J. Carey, Jr.6.3k 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> 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> 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 > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Vincent J. Carey, Jr.6.3k
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]]
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