[BioC] error when using pdInfoBuilder
James W. MacDonald
jmacdon at uw.edu
Mon May 20 23:44:07 CEST 2013
Hi Paul,
On 5/20/2013 5:23 PM, Paul Sanfilippo wrote:
> Thanks a lot Jim,
>
> I tried adding in the other arguments, but it doesn't seem to have
> made any difference. I've included a traceback() if that's of any
> value to you or anyone else who may be able to help.
>
> Thanks again.
>
> Regards,
>
> Paul
>
> > baseDir<-"/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1 Files/"
> > (pgf <- list.files(baseDir, pattern = ".pgf", full.names = TRUE))
> [1] "/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1
> Files//RaGene-2_1-st.pgf"
> > (clf <- list.files(baseDir, pattern = ".clf", full.names = TRUE))
> [1] "/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1
> Files//RaGene-2_1-st.clf"
> > (probe <- list.files(baseDir, pattern = ".probeset.csv", full.names
> = TRUE))
> [1] "/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1
> Files//RaGene-2_1-st-v1.na33.2.rn4.probeset.csv"
> > (core <- list.files(baseDir, pattern = ".mps", full.names = TRUE))
> [1] "/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1
> Files//RaGene-2_1-st.mps"
> > (trans <- list.files(baseDir, pattern = ".transcript.csv",
> full.names = TRUE))
> [1] "/Volumes/Macintosh HD2/No Backup/Affy Data/RaGene 2.1
> Files//RaGene-2_1-st-v1.na33.2.rn4.transcript.csv"
> >
> > seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile =
> clf,probeFile = probe, transFile = trans, coreMps = core, author="Paul
> Sanfilippo", email="prseye at gmail.com", biocViews="AnnotationData",
> organism = "Rat", species = "Rattus norvegicus")
> >
> >
> > makePdInfoPackage(seed, destDir = ".")
> ==========================================================================================================================================================
> Building annotation package for Affymetrix Gene ST Array
> PGF.........: RaGene-2_1-st.pgf
> CLF.........: RaGene-2_1-st.clf
> Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
> Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
> Core MPS....: RaGene-2_1-st.mps
> ==========================================================================================================================================================
> Parsing file: RaGene-2_1-st.pgf... OK
> Parsing file: RaGene-2_1-st.clf... OK
> Creating initial table for probes... Error in
> .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]) :
> NA/NaN argument
>
> > traceback()
> 8: mapply(":", starts, ends, SIMPLIFY = FALSE)
> 7: .idxToIdx(pgf[["probesetStartAtom"]], pgf[["atomId"]], probesetIdx)
> 6: probesetIdxToAtomIdx(pgf, probesetIdx)
> 5: probesetIdxToTripletIdx(pgf, 1:length(pgf[["probesetId"]]))
> 4: parsePgfClf(pgfFile = pgfFile, clfFile = clfFile, verbose = verbose)
> 3: combinePgfClfProbesetsMps(object at pgfFile, object at clfFile,
> object at probeFile,
> object at coreMps, object at fullMps, object at extendedMps, verbose =
> !quiet,
> geneArray = geneArray)
> 2: makePdInfoPackage(seed, destDir = ".")
> 1: makePdInfoPackage(seed, destDir = ".")
Looks like there might be a problem with one or more of the library
files (pgf, clf, mps). Try re-downloading and see if that helps.
Best,
Jim
>
>> James W. MacDonald <mailto:jmacdon at uw.edu>
>> 21 May 2013 3:44 AM
>> Hi Paul,
>>
>> On 5/20/2013 2:38 AM, Paul Sanfilippo [guest] wrote:
>>> Hi,
>>>
>>> This is my first attempt at analysing some expression data and I'm
>>> having trouble trying to create an annotation package using
>>> pdInfoBuilder for some rat array data. I've downloaded the
>>> appropriate library files from the affymetrix website, but encounter
>>> the following error (which I am unsure how to fix):
>>>
>>> Thanks for any suggestions.
>>>
>>> Regards,
>>>
>>> Paul
>>>
>>>
>>>
>>>> seed<- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile =
>>>> clf,probeFile = probe, transFile = trans, coreMps = core)
>>
>> You might send the results from traceback() after the error. Note
>> that I can get this to run, but I am also including the arguments for
>>
>> author
>> version
>> email
>> organism
>> species
>>
>> > seed <- new("AffyGenePDInfoPkgSeed", pgfFile = fls[29], clfFile =
>> fls[27], coreMps = fls[28], probeFile=fls[30], transFile=fls[32],
>> author="James W. MacDonald", email="jmacdon at u.washington.edu",
>> biocViews="AnnotationData", organism = "Rat", species = "Rattus
>> norvegicus")
>> > makePdInfoPackage(seed, destDir = ".")
>> ================================================================================
>>
>> Building annotation package for Affymetrix Gene ST Array
>> PGF.........: RaGene-2_1-st.pgf
>> CLF.........: RaGene-2_1-st.clf
>> Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
>> Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
>> Core MPS....: RaGene-2_1-st.mps
>> ================================================================================
>>
>> Parsing file: RaGene-2_1-st.pgf... OK
>> Parsing file: RaGene-2_1-st.clf... OK
>> Creating initial table for probes... OK
>> Creating dictionaries... OK
>> Parsing file: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv... OK
>> Parsing file: RaGene-2_1-st.mps... OK
>> Creating package in ./pd.ragene.2.1.st
>> Inserting 2640 rows into table chrom_dict... OK
>> Inserting 5 rows into table level_dict... OK
>> Inserting 11 rows into table type_dict... OK
>> Inserting 221214 rows into table core_mps... OK
>> Inserting 220231 rows into table featureSet... OK
>> Inserting 675529 rows into table pmfeature... OK
>> Counting rows in chrom_dict
>> Counting rows in core_mps
>> Counting rows in featureSet
>> Counting rows in level_dict
>> 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
>> Saving DataFrame object for PM.
>> Saving NetAffx Annotation... OK
>> Done.
>>
>> I have the same versions as you.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>>>
>>>> makePdInfoPackage(seed, destDir = ".")
>>> ==========================================================================================================================================================
>>>
>>> Building annotation package for Affymetrix Gene ST Array
>>> PGF.........: RaGene-2_1-st.pgf
>>> CLF.........: RaGene-2_1-st.clf
>>> Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
>>> Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
>>> Core MPS....: RaGene-2_1-st.mps
>>> ==========================================================================================================================================================
>>>
>>> Parsing file: RaGene-2_1-st.pgf... OK
>>> Parsing file: RaGene-2_1-st.clf... OK
>>> Creating initial table for probes... Error in
>>> .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]) :
>>> NA/NaN argument
>>>
>>> -- output of sessionInfo():
>>>
>>>> sessionInfo()
>>> R version 3.0.0 (2013-04-03)
>>> Platform: x86_64-apple-darwin10.8.0 (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] parallel stats graphics grDevices utils datasets
>>> methods base
>>>
>>> other attached packages:
>>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0
>>> affxparser_1.32.0 RSQLite_0.11.3 DBI_0.2-7
>>> Biobase_2.20.0
>>> [8] BiocGenerics_0.6.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.28.0 BiocInstaller_1.10.1
>>> Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8
>>> ff_2.2-11
>>> [7] foreach_1.4.0 GenomicRanges_1.12.4
>>> IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0
>>> splines_3.0.0
>>> [13] stats4_3.0.0 tools_3.0.0 zlibbioc_1.6.0
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> Paul Sanfilippo [guest] <mailto:guest at bioconductor.org>
>> 20 May 2013 4:38 PM
>> Hi,
>>
>> This is my first attempt at analysing some expression data and I'm having trouble trying to create an annotation package using pdInfoBuilder for some rat array data. I've downloaded the appropriate library files from the affymetrix website, but encounter the following error (which I am unsure how to fix):
>>
>> Thanks for any suggestions.
>>
>> Regards,
>>
>> Paul
>>
>>
>>
>>> seed<- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf,probeFile = probe, transFile = trans, coreMps = core)
>>>
>>> makePdInfoPackage(seed, destDir = ".")
>> ==========================================================================================================================================================
>> Building annotation package for Affymetrix Gene ST Array
>> PGF.........: RaGene-2_1-st.pgf
>> CLF.........: RaGene-2_1-st.clf
>> Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
>> Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
>> Core MPS....: RaGene-2_1-st.mps
>> ==========================================================================================================================================================
>> Parsing file: RaGene-2_1-st.pgf... OK
>> Parsing file: RaGene-2_1-st.clf... OK
>> Creating initial table for probes... Error in .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]) :
>> NA/NaN argument
>>
>> -- output of sessionInfo():
>>
>>> sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-apple-darwin10.8.0 (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] parallel stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] pdInfoBuilder_1.24.0 oligo_1.24.0 oligoClasses_1.22.0 affxparser_1.32.0 RSQLite_0.11.3 DBI_0.2-7 Biobase_2.20.0
>> [8] BiocGenerics_0.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.28.0 BiocInstaller_1.10.1 Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 ff_2.2-11
>> [7] foreach_1.4.0 GenomicRanges_1.12.4 IRanges_1.18.1 iterators_1.0.6 preprocessCore_1.22.0 splines_3.0.0
>> [13] stats4_3.0.0 tools_3.0.0 zlibbioc_1.6.0
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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