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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