Question: [R] Issue for reading .cel file (affy, affyio, oligo, affxparser)
0
gravatar for GH_fr
8 months ago by
GH_fr0
GH_fr0 wrote:

Hi there,

I got a problem when trying to read in a .cel file using different package. I tried with the package "affy" "oligo" and "affyio".

  • For "affy" and "oligo", It failed and I got the error,

    Error in read.celfile.header(x) : 
    Is C:/Users/XXX/Desktop/aaa.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats
    
  • For "affxparser", It failed and I got the error :

    Error in affxparser::readCelHeader("C:/Users/XXX/Desktop/aaa.CEL") : 
    [affxparser Fusion SDK exception] Failed to parse header of CEL file: C:/Users/XXX/Desktop/aaa.CEL
    
  • Also, I tried the command read.celfile in package "affyio" and it works fine (I think).

    List of 6
     $ HEADER      :List of 9
      ..$ cdfName            : chr "cdf_file.cdf"
      ..$ CEL dimensions     : int [1:2] 389 389
      ..$ GridCornerUL       : int [1:2] 0 0
      ..$ GridCornerUR       : int [1:2] 388 0
      ..$ GridCornerLR       : int [1:2] 388 388
      ..$ GridCornerLL       : int [1:2] 0 388
      ..$ DatHeader          : chr ""
      ..$ Algorithm          : chr "HT Image Calibration Cell Generation"
      ..$ AlgorithmParameters: chr "Percentile:75;CellMargin:4;OutlierHigh:1.500000;OutlierLow:1.004000;AlgVersion:;FixedCellSize:TRUE;FullFeatureW"| __truncated__
     $ INTENSITY   :List of 2
      ..$ :List of 3
      .. ..$ MEAN   : num [1:151321] 223 3774 219 3807 122 ...
      .. ..$ STDEV  : num [1:151321] 32.4 310.8 19.5 80.3 4.1 ...
      .. ..$ NPIXELS: num [1:151321] 9 9 9 9 9 9 9 9 9 9 ...
      ..$ :List of 3
      .. ..$ MEAN   : num [1:151321] 76 1582 84 1515 58 ...
      .. ..$ STDEV  : num [1:151321] 11.6 104.6 6.8 92.9 4.8 ...
      .. ..$ NPIXELS: num [1:151321] 9 9 9 9 9 9 9 9 9 9 ...
     $ MASKS       :List of 2
      ..$ : int[0 , 1:2] 
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : NULL
      .. .. ..$ : chr [1:2] "X" "Y"
      ..$ : int[0 , 1:2] 
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : NULL
      .. .. ..$ : chr [1:2] "X" "Y"
     $ OUTLIERS    :List of 2
      ..$ : int [1:1399, 1:2] 46 80 98 192 194 62 123 28 78 132 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : NULL
      .. .. ..$ : chr [1:2] "X" "Y"
      ..$ : int [1:2306, 1:2] 140 2 8 43 103 111 129 43 130 170 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : NULL
      .. .. ..$ : chr [1:2] "X" "Y"
     $ MULTICHANNEL: logi TRUE
     $ CHANNELNAMES: chr [1:2] "531" "609"
    

Moreover, I have a CDF file, but this file isn't recognize by the package make.cdf.package.

Reading CDF file. Error in getInfoInFile(file, "CDF", unit = "Chip",    property = "Name", : The file C:/Users/XXX/Desktop/cdf_file.cdf does    not appear to be a CDF file.

What is the problem ? is that because of the cel file type?

Any help will be highly appreciated!

cel affy R • 207 views
ADD COMMENTlink modified 8 months ago by Ram32k • written 8 months ago by GH_fr0
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