Have a look here: http://aroma-project.org/setup/
/Henrik On Wed, Sep 18, 2013 at 8:54 AM, <fenghuijuan0...@gmail.com> wrote: > Hi, I am dealing with Affy exon array data using aroma.affymetrix and had > some problems while loading CEL files, see the following code: > > >> cdf <- >> AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2",tags="coreR3,A20071112,EP") >> cdf > AffymetrixCdfFile: > Path: annotationData/chipTypes/HuEx-1_0-st-v2 > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf > File size: 38.25 MB (40108891 bytes) > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2560x2560 > Number of cells: 6553600 > Number of units: 18708 > Cells per unit: 350.31 > Number of QC units: 1 >> cs <- AffymetrixCelSet$byName("try",cdf=cdf) > Exception: Failed to setup a data set for any of 1 data directories > located. The following reasons were reported: (1) a character vector > argument expected (while trying 'rawData/try/HuEx-1_0-st-v2'). > > at #03. byName.AffymetrixCelSet(static, ...) > - byName.AffymetrixCelSet() is in environment 'aroma.affymetrix' > > at #02. byName(static, ...) > - byName() is in environment 'R.filesets' > - originating from '<text>' > > at #01. AffymetrixCelSet$byName("LNCaP", cdf = cdf) > - AffymetrixCelSet$byName() is local of the calling function > > Error: Failed to setup a data set for any of 1 data directories located. The > following reasons were reported: (1) a character vector argument expected > (while trying 'rawData/try/HuEx-1_0-st-v2'). > > See the R session. > >> sessionInfo() > R version 3.0.1 RC (2013-05-12 r62742) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomeGraphs_1.20.0 biomaRt_2.16.0 aroma.light_1.30.2 > [4] matrixStats_0.8.10 aroma.affymetrix_2.10.0 aroma.core_2.10.1 > [7] R.devices_2.5.0 R.filesets_2.1.0 R.utils_1.27.1 > [10] R.oo_1.15.1 affxparser_1.32.1 R.methodsS3_1.5.1 > > loaded via a namespace (and not attached): > [1] PSCBS_0.35.6 R.cache_0.7.1 R.huge_0.5.0 R.rsp_0.9.17 > [5] RCurl_1.95-4.1 XML_3.98-1.1 aroma.apd_0.3.0 digest_0.6.3 > [9] tools_3.0.1 > > Could anybody give me some sign on this error? Thanks very much. > > > > > > > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.