[BioC] An error in oligo: All the CEL files must be of the same type??

[Benilton Carvalho]

For the record: the problem was solved once the user used the
annotation package available through BioConductor.

b

On 13 June 2011 16:25, Setsuko Sahara <sahara at salk.edu> wrote:
> Dear Benilton
> Thank you so much for your suggestion. Yes, the error says my files are not
> mogene 1.0 st r4, but the wired thing is that I was able to obtain the
> results with the same set of CEL files a month ago...
> I'll try your 2nd suggestion!
> setsu
> On Jun 10, 2011, at 4:10 PM, Benilton Carvalho wrote:
>
> That is telling you that not all the  files are mogene 1.0 st r4. Is this
> the case? If you're trying to force oligo to read a set of samples whose
> header does not match an available annotation package, you should use the
> pkgname argument and pass the name of the package you want it to use.
>
> B
>
> On 10 Jun 2011 23:50, "Setsuko Sahara" <sahara at salk.edu> wrote:
>
> Hello all,
>
> I'm a new to bioconductor and encounter an error when I use oligo for the
> analysis of affymetrix mouse Gene 1.0 ST array.
> A month ago when I set up oligo with GEO data, it worked perfectly, but
> started having a problem when the function of read.celfiles.
> No matter the files are ( mine or GEO one that had worked fine), now I
> always see an error  as
> "All the CEL files must be of the same type.
> Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not
> TRUE"....
>
> So I'm wondering if anyone has any idea what would be wrong?
>
> Here is a script.
>
> Thank you very much for your comments in advance!
>
> Best,
>
>> library(pdInfoBuilder)
>> baseDir <-
>> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene"
>> (pgf <- list.files(baseDir, pattern = ".pgf",
> + full.names = TRUE))
> [1]
> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene/MoGene-1_0-st-v1.r4.pgf"
>> (clf <- list.files(baseDir, pattern = ".clf",
> + full.names = TRUE))
> [1]
> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene/MoGene-1_0-st-v1.r4.clf"
>> (prob <- list.files(baseDir, pattern = ".probeset.csv",
> + full.names = TRUE))
> [1]
> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene/MoGene-1_0-st-v1.na31.mm9.probeset.csv"
>> (transcript <- list.files(baseDir, pattern = ".transcript.csv",
> + full.names = TRUE))
> [1]
> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene/MoGene-1_0-st-v1.na31.mm9.transcript.csv"
>> (coreMps <- list.files(baseDir, pattern = ".mps",
> + full.names = TRUE))
> [1]
> "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGene/MoGene-1_0-st-v1.r4.mps"
>> seed <- new("AffyGenePDInfoPkgSeed",
> + pgfFile = pgf, clfFile = clf,
> + probeFile = prob, transFile = transcript, coreMps = coreMps, author =
> "setsu sahara",
> + email = "sahara at salk.edu",
> + biocViews = "AnnotationData",
> + organism = "Mouse", species = "mouse",
> + url = "http://www.salk.edu")
>> makePdInfoPackage(seed, destDir = ".")
> =========================================================================================
> Building annotation package for Affymetrix Gene ST Array
> PGF.........: MoGene-1_0-st-v1.r4.pgf
> CLF.........: MoGene-1_0-st-v1.r4.clf
> Probeset....: MoGene-1_0-st-v1.na31.mm9.probeset.csv
> Transcript..: MoGene-1_0-st-v1.na31.mm9.transcript.csv
> Core MPS....: MoGene-1_0-st-v1.r4.mps
> =========================================================================================
> Parsing file: MoGene-1_0-st-v1.r4.pgf... OK
> Parsing file: MoGene-1_0-st-v1.r4.clf... OK
> Creating initial table for probes... OK
> Creating dictionaries... OK
> Parsing file: MoGene-1_0-st-v1.na31.mm9.probeset.csv... OK
> Parsing file: MoGene-1_0-st-v1.r4.mps... OK
> Creating package in ./pd.mogene.1.0.st.v1
> Inserting 44 rows into table chrom_dict... OK
> Inserting 5 rows into table level_dict... OK
> Inserting 8 rows into table type_dict... OK
> Inserting 241576 rows into table core_mps... OK
> Inserting 241576 rows into table featureSet... OK
> Inserting 899636 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.
> Warning messages:
> 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
> 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>> library(oligo)
>> library(pdInfoBuilder)
>> geneCELs <- list.celfiles("Users/setsukosahara/data/Affy/oligo/CEL
>> files/Fgf10 cell files", full.names = TRUE)
>> affyGeneFS <- read.celfiles(geneCELs)
> All the CEL files must be of the same type.
> Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE
>>
>
> Setsuko Sahara
> Senior Research Associate
> Molecular Neurobiology Laboratory (MNL-O)
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA 92037  USA
> Tel:(858) 453-4100 ext.1449
> Fax:(858) 558-6207
>
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>
>
> Setsuko Sahara
> Senior Research Associate
> Molecular Neurobiology Laboratory (MNL-O)
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA 92037  USA
> Tel:(858) 453-4100 ext.1449
> Fax:(858) 558-6207
>
>
>



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