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 website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/