*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.
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