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/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

	[[alternative HTML version deleted]]

