[BioC] read cel file of moe430a

[Ben Bolstad]

That does not seem to be a desirable situation. Given you have what
looks to be a text format CEL file and that the parsers in affyio have
been used with 1000s of text format CEL files (of many different chip
types), it seems somewhat unlikely that it is an error in the parsing
code, rather than some malformation of the CEL file.

But, if you would like to send me this CEL file (off-list of course) I
could examine it further.

best,

Ben


On Mon, 2009-06-29 at 10:47 -0400, Ming-Chung Li wrote:
> Dear All,
>  
> I have a problem of reading cel files from MOE430A type. The error I get is 
> 
> > library(affy)
> > res=justRMA()
>  
> Error in just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description,  : 
> 
>  Is c:/temp/mouse430a/Green.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats
> 
>  
> 
> 
> The first few lines of the cel file look like
>  
> [CEL]
> 
> Version=3
>  
> [HEADER]
> 
> Cols=712
> 
> Rows=712
> 
> TotalX=712
> 
> TotalY=712
> 
> OffsetX=0
> 
> OffsetY=0
> 
> GridCornerUL=228 231
> 
> GridCornerUR=4490 217
> 
> GridCornerLR=4497 4487
> 
> GridCornerLL=235 4501
> 
> Axis-invertX=0
> 
> AxisInvertY=0
> 
> swapXY=0
> 
> DatHeader=[0..46130]  Control 1 rerun:CLS=4733 RWS=4733 XIN=3  YIN=3  VE=17        2.0 02/07/04 11:41:58     MOE430A.1sq         6
> 
> Algorithm=Percentile
> 
> AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004
>  
> [INTENSITY]
> 
> NumberCells=506944
> 
> 
> My sessionInfo is 
> 
> R version 2.9.0 (2009-04-17) 
> 
> i386-pc-mingw32 
> 
> locale:
> 
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>  
> attached base packages:
> 
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods  
> 
> [8] base     
> 
> other attached packages:
> 
> [1] affy_1.22.0     Biobase_2.4.1   svGUI_0.9-43    svSocket_0.9-42
> 
> [5] svMisc_0.9-45  
> 
> loaded via a namespace (and not attached):
> 
> [1] affyio_1.12.0        preprocessCore_1.6.0
> 
> 
> I appreicate any help. Thanks,
>  
> Ming-chung Li
>  
> 
> 
> 
> 
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> 
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