This looks all correct to me. What is your sessionInfo() after
receiving this error?
/Henrik
On Wed, Oct 15, 2014 at 4:19 AM, sanjana <sood.sanj...@gmail.com> wrote:
> Hi,
>
> I am using a Custom cdf file HTA-2_0,Transcript,binary.cdf in aroma.
> affymetrix to analyse HTA-2_0 chip . I am using the following commands to
> set up CDF and CEL files.
>
>>chipType <- "HTA-2_0"
>>cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Transcript,binary")
>>print(cdf)
>
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HTA-2_0
> Filename: HTA-2_0,Transcript,binary.cdf
> File size: 7.55 MB (7921066 bytes)
> Chip type: HTA-2_0,Transcript,binary
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 18490
> Cells per unit: 354.44
> Number of QC units: 0
>
>>cs<-AffymetrixCelSet$byName("Krzy",cdf=cdf,verbose=verbose)
>
> However I am unable to read the CEL files as it gives me the following
> error:
>
> Error: Failed to setup a data set for any of 1 data directories located. The
> following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'HTA-2_0'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/Krzy/HTA-2_0').
>
> My directory structure is:
> annotationData< chipTypes<HTA-2_0<HTA-2_0,Transcript,binary.cdf
> rawData<Krzy<HTA-2_0<K15P.CEL
>
> Please can someone help me understanding what I am doing wrong. I have used
> aroma.affymetrix for exon arrays and I never came across this issue. Is it
> something to do with the CDF file?
>
>
> Kind Regards,
> Sanjana
>
>
>
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version of the package, 2) to report the output of sessionInfo() and
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