Hi,
unfortunately there is no option to turn off locating *.saf files part
of the package installation (I'll see if I can add one for the next
release). However, it's strange if that would be the cause for you
problem, but on the other hand strange things happens all the time.
For troubleshooting, see what the following does:
sas <- SampleAnnotationSet$loadAll(verbose=-5);
print(sas);
for (kk in seq(sas)) {
saf <- getFile(sas, kk);
print(saf);
df <- readDataFrame(saf, verbose=-5);
str(df);
} # for (kk ...)
Do you get an error? If so, for what file? Please provide a
traceback() report upon errors. Does the other SAF files work, i.e.
if you try manually with different 'kk':s will they load?
Cheers,
Henrik
On Thu, May 5, 2011 at 9:00 AM, richland <yiping.f...@gmail.com> wrote:
> Hi,list,
>
>
> Here is my basic set up under my current working directory:~/project/
>
> rawData/M7/GenomeWideSNP_6/
> 23..CEL SJO023-snp6.CEL 25-snp6.CEL,26-snp6.CEL ...
>
> ==
> annotationData/chipTypes/GenomeWideSNP_6/
>
> GenomeWideSNP_6,Full.cdf
> GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
> GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
> GenomeWideSNP_6,HB20080710.acs
>
> I don't need sample information so there is no samples/ directory
> under annotationData
>
> I'm using R/2.12.0, aroma.affymetrix v2.1.0 (2011-04-08)
>
> #
> ibrary(aroma.affymetrix)
> verbose <- Arguments$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!
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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