Question: Affy HTA 2.0 array analysis
0
gravatar for He, Yiwen NIH/CIT
5.6 years ago by
He, Yiwen NIH/CIT360 wrote:
Hi, I am trying to analyze the affy HTA 2.0 array. I tried to create the pd.hta.2.0 package using makePdInfoPackage() in the pdInfoBuilder package, and got a message saying data type mismatch. I searched the archive and saw people with the same problem, but no solutions. Can someone please help? I am using R 3.0.1 and all packages are updated. Thank you! Yiwen NIH/CIT --------------------------------------- library(pdInfoBuilder) pgf <- "HTA-2_0.r1.pgf" clf <- "HTA-2_0.r1.clf" probe <- "HTA-2_0.na33.hg19.probeset.csv" transcript <- "HTA-2_0.na33.hg19.transcript.csv" mps <- "HTA-2_0.r1.Psrs.mps" seed <- new("AffyGenePDInfoPkgSeed", pgfFile=pgf, clfFile=clf, probeFile=probe, transFile=transcript, coreMps=mps) 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..: HTA-2_0.na33.hg19.transcript.csv 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)
annotation affy • 2.0k views
ADD COMMENTlink modified 3.9 years ago by Jason Hubbard20 • written 5.6 years ago by He, Yiwen NIH/CIT360
Answer: Affy HTA 2.0 array analysis
1
gravatar for Jason Hubbard
3.9 years ago by
Seattle, WA
Jason Hubbard20 wrote:

In case someone comes here with the same question, you can find the pdinfo package here:

http://www.bioconductor.org/packages/release/data/annotation/html/pd.hta.2.0.html

ADD COMMENTlink written 3.9 years ago by Jason Hubbard20
Answer: Affy HTA 2.0 array analysis
0
gravatar for Benilton Carvalho
5.6 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Not yet supported, but thinking of a solution. 2013/9/13 He, Yiwen (NIH/CIT) [C] <heyiwen@mail.nih.gov> > Hi, > > I am trying to analyze the affy HTA 2.0 array. I tried to create the > pd.hta.2.0 package using makePdInfoPackage() in the pdInfoBuilder package, > and got a message saying data type mismatch. I searched the archive and saw > people with the same problem, but no solutions. Can someone please help? I > am using R 3.0.1 and all packages are updated. Thank you! > > Yiwen > NIH/CIT > > --------------------------------------- > library(pdInfoBuilder) > > pgf <- "HTA-2_0.r1.pgf" > clf <- "HTA-2_0.r1.clf" > probe <- "HTA-2_0.na33.hg19.probeset.csv" > transcript <- "HTA-2_0.na33.hg19.transcript.csv" > mps <- "HTA-2_0.r1.Psrs.mps" > > seed <- new("AffyGenePDInfoPkgSeed", > pgfFile=pgf, clfFile=clf, > probeFile=probe, > transFile=transcript, > coreMps=mps) > > 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..: HTA-2_0.na33.hg19.transcript.csv > 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) > > _______________________________________________ > 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 5.6 years ago by Benilton Carvalho4.3k
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