Dear Benilton, thanks for your e-mail. I'm sorry for not having writed back till now, but I have just read it (I don't know why it was not labelled, so I lost it among all the others from bioconductor....) I will try to analyze the arrays I have pending with your script. I will write back soon! Thank you again! Best regards, Elena 2013-11-18 18:44 GMT+01:00 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]]