Hi there,

I got a problem when trying to read in a .cel file using ReadAffy().

R codes:

require(affy)
ReadAffy(filenames="CH1.CEL")

It failed and I got the error,

Error in read.celfile.header(as.character(filenames[[1]])) :
  Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary,
gzipped binary, command console and gzipped command console formats

Also, I tried the command read.celfile in package "affyio" and it works,

> x<-read.celfile("CH1.CEL")
> str(x)
List of 6
 $ HEADER      :List of 9
  ..$ cdfName            : chr "Axiom_GW_ASI_SNP"
  ..$ CEL dimensions     : int [1:2] 1190 1190
  ..$ GridCornerUL       : int [1:2] 0 0
  ..$ GridCornerUR       : int [1:2] 1189 0
  ..$ GridCornerLR       : int [1:2] 1189 1189
  ..$ GridCornerLL       : int [1:2] 0 1189
  ..$ DatHeader          : chr ""
  ..$ Algorithm          : chr "HT Image Calibration Cell Generation"
  ..$ AlgorithmParameters: chr
"Percentile:75;CellMargin:4;OutlierHigh:1.500000;OutlierLow:1.004000;AlgVersion:;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatu"|
__truncated__
 $ INTENSITY   :List of 2
  ..$ :List of 3
  .. ..$ MEAN   : num [1:1416100] 1309 3867 1162 4093 1153 ...
  .. ..$ STDEV  : num [1:1416100] 70 803.8 65.4 781.7 97.3 ...
  .. ..$ NPIXELS: num [1:1416100] 9 9 9 9 9 9 9 9 9 9 ...
  ..$ :List of 3
  .. ..$ MEAN   : num [1:1416100] 356 4090 345 4093 326 ...
  .. ..$ STDEV  : num [1:1416100] 35.5 246.1 23.5 328.6 41.9 ...
  .. ..$ NPIXELS: num [1:1416100] 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 [1:98480, 1:2] 18 40 44 63 66 127 154 195 196 9 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "X" "Y"
  ..$ : int [1:46039, 1:2] 83 114 173 199 2 115 181 1 3 9 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "X" "Y"
 $ MULTICHANNEL: logi TRUE
 $ CHANNELNAMES: chr [1:2] "531" "609"
 My question is
1. why ReadAffy doesn't work for this chip? is that because of the cel file
type?

2. I have some experience of ATH1121501 chip analysis, the data
structure given by read.celfile looks different from that, how to get PM/MM
values?

Any help will be highly appreciated!

Na

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