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

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@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/AffyGen e" > (pgf <- list.files(baseDir, pattern = ".pgf", + full.names = TRUE)) [1] "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGen e/MoGene-1_0-st-v1.r4.pgf" > (clf <- list.files(baseDir, pattern = ".clf", + full.names = TRUE)) [1] "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyGen e/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/AffyGen e/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/AffyGen e/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/AffyGen e/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@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 _______________________________________________ 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]]

something definitely changed.... either the set of CEL files or the call you made to oligo. i noticed that you're creating your own annotation package... any reason you're not using the one we provide via 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/Affy Gene" >> (pgf <- list.files(baseDir, pattern = ".pgf", > + full.names = TRUE)) > [1] > "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyG ene/MoGene-1_0-st-v1.r4.pgf" >> (clf <- list.files(baseDir, pattern = ".clf", > + full.names = TRUE)) > [1] > "/Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/AffyG ene/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/AffyG ene/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/AffyG ene/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/AffyG ene/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 > > _______________________________________________ > 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 > > > 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 > > > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)