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.
>
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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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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