Question: Draft support for HTA 2.0 with oligo
0
gravatar for Johann Pellet
5.8 years ago by
Johann Pellet10 wrote:
Dear Benilton, thanks for this first draft support for the HTA 2.0 chip. I tried to follow your workflow using your annotation package specific for HTA or one built through pdInfoBuilder. For both I can not use the package pd.hta.2.0, see below. > library(oligo) > install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0.zip", repos = NULL) > library(pd.hta.2.0) Error in library(pd.hta.2.0) : ?pd.hta.2.0? is not a valid installed package > raw = read.celfiles(phenoData="Raw/phenodataHTA2.txt",verbose=TRUE, filenames=cels) Loading required package: pd.hta.2.0 Failed with error: ??pd.hta.2.0? is not a valid installed package? Attempting to obtain 'pd.hta.2.0' from BioConductor website. Checking to see if your internet connection works... Package 'pd.hta.2.0' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in read.celfiles(phenoData = "Raw/phenodataHTA2.txt", verbose = TRUE, : The annotation package, pd.hta.2.0, could not be loaded. ###### More info > sessionInfo() R Under development (unstable) (2014-02-27 r65090) Platform: x86_64-w64-mingw32/x64 (64-bit) attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.27.5 oligo_1.27.9 Biostrings_2.31.14 XVector_0.3.7 [5] IRanges_1.21.32 oligoClasses_1.25.6 affxparser_1.35.0 RSQLite_0.11.4 [9] DBI_0.2-7 Biobase_2.23.5 BiocGenerics_0.9.3 BiocInstaller_1.13.3 loaded via a namespace (and not attached): [1] affyio_1.31.0 bit_1.1-11 codetools_0.2-8 ff_2.2-12 [5] foreach_1.4.1 GenomicRanges_1.15.31 iterators_1.0.6 preprocessCore_1.25.5 [9] splines_3.1.0 stats4_3.1.0 tools_3.1.0 zlibbioc_1.9.0 > > makePdInfoPackage(seed, destDir=".") ====================================================================== ======================= Building annotation package for Affymetrix HTA 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 14 rows into table type_dict... OK Inserting 577432 rows into table core_mps... OK Inserting 925032 rows into table featureSet... OK Inserting 7576209 rows into table pmfeature... OK Inserting 1121 rows into table mmfeature... OK Counting rows in chrom_dict Counting rows in core_mps Counting rows in featureSet Counting rows in level_dict Counting rows in mmfeature Counting rows in pmfeature Counting rows in type_dict Creating index idx_pmfsetid on pmfeature... OK Creating index idx_pmfid on pmfeature... OK Creating index idx_fsfsetid on featureSet... OK Creating index idx_core_meta_fsetid on core_mps... OK Creating index idx_core_fsetid on core_mps... OK Creating index idx_mmfsetid on mmfeature... OK Creating index idx_mmfid on mmfeature... OK Saving DataFrame object for PM. Saving DataFrame object for MM. Saving NetAffx Annotation... OK Done.
annotation pdinfobuilder • 1.8k views
ADD COMMENTlink modified 3.4 years ago by aswathym0 • written 5.8 years ago by Johann Pellet10
Answer: Draft support for HTA 2.0 with oligo
0
gravatar for James W. MacDonald
5.8 years ago by
United States
James W. MacDonald52k wrote:
Hi Johann, On 2/28/2014 12:05 PM, Johann Pellet wrote: > Dear Benilton, > > thanks for this first draft support for the HTA 2.0 chip. > > I tried to follow your workflow using your annotation package specific for HTA or one built through pdInfoBuilder. For both I can not use the package pd.hta.2.0, see below. > >> library(oligo) >> install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0.zip", repos = NULL) >> library(pd.hta.2.0) > Error in library(pd.hta.2.0) : > ?pd.hta.2.0? is not a valid installed package If I were to guess, I would bet that you built the package and then used something like WinZip to create a zip file. If so, you can't do that. Instead you want to do install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0", repos=NULL, type = "source") Best, Jim > > >> raw = read.celfiles(phenoData="Raw/phenodataHTA2.txt",verbose=TRUE, filenames=cels) > Loading required package: pd.hta.2.0 > Failed with error: ??pd.hta.2.0? is not a valid installed package? > Attempting to obtain 'pd.hta.2.0' from BioConductor website. > Checking to see if your internet connection works... > Package 'pd.hta.2.0' was not found in the BioConductor repository. > The 'pdInfoBuilder' package can often be used in situations like this. > Error in read.celfiles(phenoData = "Raw/phenodataHTA2.txt", verbose = TRUE, : > The annotation package, pd.hta.2.0, could not be loaded. > > > ###### More info > >> sessionInfo() > R Under development (unstable) (2014-02-27 r65090) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pdInfoBuilder_1.27.5 oligo_1.27.9 Biostrings_2.31.14 XVector_0.3.7 > [5] IRanges_1.21.32 oligoClasses_1.25.6 affxparser_1.35.0 RSQLite_0.11.4 > [9] DBI_0.2-7 Biobase_2.23.5 BiocGenerics_0.9.3 BiocInstaller_1.13.3 > > loaded via a namespace (and not attached): > [1] affyio_1.31.0 bit_1.1-11 codetools_0.2-8 ff_2.2-12 > [5] foreach_1.4.1 GenomicRanges_1.15.31 iterators_1.0.6 preprocessCore_1.25.5 > [9] splines_3.1.0 stats4_3.1.0 tools_3.1.0 zlibbioc_1.9.0 > > >> makePdInfoPackage(seed, destDir=".") > ==================================================================== ========================= > Building annotation package for Affymetrix HTA 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 14 rows into table type_dict... OK > Inserting 577432 rows into table core_mps... OK > Inserting 925032 rows into table featureSet... OK > Inserting 7576209 rows into table pmfeature... OK > Inserting 1121 rows into table mmfeature... OK > Counting rows in chrom_dict > Counting rows in core_mps > Counting rows in featureSet > Counting rows in level_dict > Counting rows in mmfeature > Counting rows in pmfeature > Counting rows in type_dict > Creating index idx_pmfsetid on pmfeature... OK > Creating index idx_pmfid on pmfeature... OK > Creating index idx_fsfsetid on featureSet... OK > Creating index idx_core_meta_fsetid on core_mps... OK > Creating index idx_core_fsetid on core_mps... OK > Creating index idx_mmfsetid on mmfeature... OK > Creating index idx_mmfid on mmfeature... OK > Saving DataFrame object for PM. > Saving DataFrame object for MM. > Saving NetAffx Annotation... OK > Done. > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.8 years ago by James W. MacDonald52k
Answer: Draft support for HTA 2.0 with oligo
0
gravatar for Benilton Carvalho
5.8 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
After building the package, as you showed on your email, you should be able to install it just by using: install.packages('pd.hta.2.0', repo=NULL) Then, for reading the celfiles, do not give a txt file as input for phenoData. I may need to fix the code, but in the meantime use something like: library(oligo) cels = list.files() raw = read.celfiles(cels) pd = read.AnnotatedDataFrame('Raw/phenodataHTA2.txt') phenoData(raw) = pd benilton 2014-02-28 14:05 GMT-03:00 Johann Pellet <jpellet@eisbm.org>: > Dear Benilton, > > thanks for this first draft support for the HTA 2.0 chip. > > I tried to follow your workflow using your annotation package specific for > HTA or one built through pdInfoBuilder. For both I can not use the package > pd.hta.2.0, see below. > > > library(oligo) > > install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0.zip", repos = NULL) > > library(pd.hta.2.0) > Error in library(pd.hta.2.0) : > ëpd.hta.2.0í is not a valid installed package > > > > raw = read.celfiles(phenoData="Raw/phenodataHTA2.txt",verbose=TRUE, > filenames=cels) > Loading required package: pd.hta.2.0 > Failed with error: ëëpd.hta.2.0í is not a valid installed packageí > Attempting to obtain 'pd.hta.2.0' from BioConductor website. > Checking to see if your internet connection works... > Package 'pd.hta.2.0' was not found in the BioConductor repository. > The 'pdInfoBuilder' package can often be used in situations like this. > Error in read.celfiles(phenoData = "Raw/phenodataHTA2.txt", verbose = > TRUE, : > The annotation package, pd.hta.2.0, could not be loaded. > > > ###### More info > > > sessionInfo() > R Under development (unstable) (2014-02-27 r65090) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] pdInfoBuilder_1.27.5 oligo_1.27.9 Biostrings_2.31.14 > XVector_0.3.7 > [5] IRanges_1.21.32 oligoClasses_1.25.6 affxparser_1.35.0 > RSQLite_0.11.4 > [9] DBI_0.2-7 Biobase_2.23.5 BiocGenerics_0.9.3 > BiocInstaller_1.13.3 > > loaded via a namespace (and not attached): > [1] affyio_1.31.0 bit_1.1-11 codetools_0.2-8 > ff_2.2-12 > [5] foreach_1.4.1 GenomicRanges_1.15.31 iterators_1.0.6 > preprocessCore_1.25.5 > [9] splines_3.1.0 stats4_3.1.0 tools_3.1.0 > zlibbioc_1.9.0 > > > > > > > makePdInfoPackage(seed, destDir=".") > > ==================================================================== ========================= > Building annotation package for Affymetrix HTA 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 14 rows into table type_dict... OK > Inserting 577432 rows into table core_mps... OK > Inserting 925032 rows into table featureSet... OK > Inserting 7576209 rows into table pmfeature... OK > Inserting 1121 rows into table mmfeature... OK > Counting rows in chrom_dict > Counting rows in core_mps > Counting rows in featureSet > Counting rows in level_dict > Counting rows in mmfeature > Counting rows in pmfeature > Counting rows in type_dict > Creating index idx_pmfsetid on pmfeature... OK > Creating index idx_pmfid on pmfeature... OK > Creating index idx_fsfsetid on featureSet... OK > Creating index idx_core_meta_fsetid on core_mps... OK > Creating index idx_core_fsetid on core_mps... OK > Creating index idx_mmfsetid on mmfeature... OK > Creating index idx_mmfid on mmfeature... OK > Saving DataFrame object for PM. > Saving DataFrame object for MM. > Saving NetAffx Annotation... OK > Done. > _______________________________________________ > 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 5.8 years ago by Benilton Carvalho4.3k
Answer: Draft support for HTA 2.0 with oligo
0
gravatar for aswathym
3.4 years ago by
aswathym0
United States
aswathym0 wrote:

I don't know whether you have tried biocLite("pd.hta.2.0")  and then loaded using the command library. It worked for without any error I could load the cel files.

ADD COMMENTlink written 3.4 years ago by aswathym0
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