Question: CDF file for Cytoscan arrays
0
gravatar for jgarces
6 months ago by
jgarces10
Spain
jgarces10 wrote:

Hi there,

I'm trying to read some CEL files from Cytoscan HD arrays with the R package affy but I get this (annoying) error:

> u <- read.affybatch(filenames = list.files(pattern=".CEL$"))
> u
    Error in getCdfInfo(object) :
      Could not obtain CDF environment, problems encountered:
    Specified environment does not contain CytoScanHD_Array
    Library - package cytoscanhdarraycdf not installed
    Bioconductor - cytoscanhdarraycdf not available
    Además: Warning message:
    missing cdf environment! in show(AffyBatch)

I've tried to build this CDF file through aroma package (from Affymetrix) and another error appears:

> cdf <- AffymetrixCdfFile$byChipType("2MO_(CytoScanHD_Array).CEL")
[2019-03-06 17:21:59] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type '2MO_(CytoScanHD_Array).CEL' (without requiring any tags) and with filename extension 'cdf'.

  at #03. byChipType.UnitAnnotationDataFile(static, ...)
          - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'

  at #02. byChipType(static, ...)
          - byChipType() is in environment 'aroma.core'
          - originating from '<text>'

  at #01. AffymetrixCdfFile$byChipType("2MO_(CytoScanHD_Array).CEL")
          - AffymetrixCdfFile$byChipType() is local of the calling function

Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type '2MO_(CytoScanHD_Array).CEL' (without requiring any tags) and with filename extension 'cdf'.

Anyone could me where can I get this CDF file? Or any way to build it, please? Or to understand the error??

Thanks in advance. Regards.

cdf cystoscan array • 309 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by jgarces10

The CDFs for these old Affymetrix arrays can be very difficult to find. A problem was that Affymetrix were purchased by ThermoFisher, and support for products was lost.

I have done a search and found these sources:

ADD REPLYlink written 6 months ago by Kevin Blighe48k

Thanks Kevin. I've downloaded the CDF file from the second link and I've move to the folder with the CELs but errors don't disappear... thanks anyway!

ADD REPLYlink written 6 months ago by jgarces10

Strange - sorry about that. I would try to contact Affymetrix (Thermo Fisher). I think that there are still some remnants of the old support teams, whether they are officially now at Thermo is another question.

ADD REPLYlink written 6 months ago by Kevin Blighe48k
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