[R] read in cel file by ReadAffy and read.celfile

[Martin Morgan]

On 08/08/2011 02:04 AM, You Na wrote:
> Hi there,
>
> I got a problem when trying to read in a .cel file using ReadAffy().
>
> R codes:
>
> require(affy)

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Martin

> 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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>
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