CDF file for Cytoscan arrays

Question

[garcesj]

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.

[Kevin Blighe]

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:

• https://bitbucket.org/brge/affy2sv/wiki/CytoScan
• http://www.affymetrix.com/support/technical/byproduct.affx?product=cytoscan_kit (look at ChAS files, at the bottom)
• https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html

[garcesj]

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!

[Kevin Blighe]

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.