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" 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@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 > 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 [[alternative HTML version deleted]]