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

[Setsuko Sahara]

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 = ".")
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========================================================================
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
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========================================================================
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