Hi, Henrik,
Thanks a lot for the quick reply. Problem solved. I ran
aroma.affymetrix before. I had a .Rcache/aroma.affymetrix in my home
directory.
Later system admin changed my uid. So when I ran aroma.affymetrix
again, I wan not able to write to that directory. That's where the
error "data set could not be setup for this path, because:
cannot open the connection" comes from.
cheers,
Richland
On May 5, 1:30 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> 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.
>
> > You received this message because you are subscribed to the Google Groups
> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
--
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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