Hi,list,
Here is my basic set up under my current working directory:~/project/
rawData/M7/GenomeWideSNP_6/
23..CEL SJO023-snp6.CEL 25-snp6.CEL,26-snp6.CEL ...
==
annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
GenomeWideSNP_6,HB20080710.acs
I don't need sample information so there is no samples/ directory
under annotationData
I'm using R/2.12.0, aroma.affymetrix v2.1.0 (2011-04-08)
#
ibrary(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8)
timestampOn(verbose)
chipType <- "GenomeWideSNP_6"
cdf<- AffymetrixCdfFile$byChipType(chipType,tags="Full")
print(cdf) # ok
dataSetName<-"M7";
cs <- AffymetrixCelSet$byName(dataSetName,
cdf=cdf, verbose=-10)
failed:
it found all 6 cell files, but keeps looking form saf file in /
nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/aroma.affymetrix/
annotationData/samples/HapMap270.saf"
########################
Trying path #1 of 1...
Path: rawData/M7/GenomeWideSNP_6
Defining AffymetrixCelSet from files...
Defining an AffymetrixCelSet object from files...
Path: rawData/M7/GenomeWideSNP_6
Pattern: [.](c|C)(e|E)(l|L)$
File class: AffymetrixCelFile
Scanning directory for files...
Found 6 files/directories.
Found 6 files.
Scanning directory for files...done
Defining 6 files...
1, 2, 3, 4, 5, 6,
Defining 6 files...done
Allocating a new AffymetrixCelSet instance...
Arguments:
Number of files: 6
list()
Allocating a new AffymetrixCelSet instance...done
Updating newly allocated AffymetrixCelSet...
Updating AffymetrixCelSet...
Scanning for and applying sample annotation files...
Loading all SampleAnnotationSet:s...
Identify all directories containing SAF files...
All SAF files located:
[1] "/nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
aroma.affymetrix/annotationData/samples/HapMap270.saf"
Path (to the first file): /nfs_exports/apps/64-bit/gnu-apps/R/
libraries/2.12.0/aroma.affymetrix/annotationData/samples
Total file size: 0.03 MB
RAM: 0.00MB
Scanning for and applying sample annotation files...done
Updating AffymetrixCelSet...done
Defining AffymetrixCelSet from files...done
Data set could not be setup for this path, because:
cannot open the connection
Trying path #1 of 1...done
Error in list(`AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose
= -10)` = <environment>, :
[2011-05-05 10:46:03] Exception: Failed to setup a data set for any of
1 data directories located.
at throw(Exception(...))
at throw.default(sprintf("Failed to setup a data set for any of %d
data direct
at throw(sprintf("Failed to setup a data set for any of %d data
directories lo
at method(static, ...)
at AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose = -10)
Calls: <Anonymous> ... method -> throw -> throw.default -> throw ->
throw.Exception
Setting up AffymetrixCelSet by name...done
Execution halted
===============
I also tried to make a samples/ directory under annotationData/ ans
made a file called M7.saf. it also failed.
[1] "rawData/M7/GenomeWideSNP_6"
Trying path #1 of 1...
Path: rawData/M7/GenomeWideSNP_6
Defining AffymetrixCelSet from files...
Defining an AffymetrixCelSet object from files...
Path: rawData/M7/GenomeWideSNP_6
Pattern: [.](c|C)(e|E)(l|L)$
File class: AffymetrixCelFile
Scanning directory for files...
Found 6 files/directories.
Found 6 files.
Scanning directory for files...done
Defining 6 files...
1, 2, 3, 4, 5, 6,
Defining 6 files...done
Allocating a new AffymetrixCelSet instance...
Arguments:
Number of files: 6
list()
Allocating a new AffymetrixCelSet instance...done
Updating newly allocated AffymetrixCelSet...
Updating AffymetrixCelSet...
Scanning for and applying sample annotation files...
Loading all SampleAnnotationSet:s...
Identify all directories containing SAF files...
All SAF files located:
[1] "annotationData/samples/
M7.saf"
[2] "/nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
aroma.affymetrix/annotationData/samples/HapMap270.saf"
It found the the M7.saf but also try to locate the other *saf files.
How to avoid this situation? Thanks!
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