Question: Affymetrix HTA 2 array analysis
0
gravatar for Stephen Turner
6.0 years ago by
United States
Stephen Turner270 wrote:
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]]
ADD COMMENTlink modified 6.0 years ago by Benilton Carvalho4.3k • written 6.0 years ago by Stephen Turner270
Answer: Affymetrix HTA 2 array analysis
0
gravatar for Benilton Carvalho
6.0 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
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]]
ADD COMMENTlink written 6.0 years ago by Benilton Carvalho4.3k
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