Entering edit mode
3.7 years ago
GH_fr
•
0
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!