[BioC] simple

[James W. MacDonald]

Hi Scott,

On 7/11/2013 7:07 AM, Scott Robinson [guest] wrote:
> Dear All,
>
> I am working on a human Affymetrix chip and have loaded the "simpleaffy" library. I am recieving the following error message upon running "read.affy()":
>
> "It appears that the file ./C_3675_31-07-09.CEL is corrupted."

This error doesn't come from simpleaffy, it comes from a dependency 
package called affyio, so you won't find anything about this in the 
simpleaffy manual.

Anyway, the error comes from various checks to ensure that the celfile 
conforms to expected dimensions (the right number of rows and columns), 
etc. And the short story is that this file won't work. Do you have 
another copy (perhaps still on the computer that runs the Affy chip 
reader)? If so, you might try getting that copy and seeing if it is 
corrupted as well. If it is, you might be able to re-process the DAT 
file to create another CEL file.

If that doesn't work, then this sample might be lost.

Best,

Jim


>
> I can not find anything about it in the simpleaffy manual and was wondering does this mean the CEL file is corrupt beyond use?
>
> I have googled about looking for an answer to what it is precisely that is wrong with the files that the read.affy() function is picking up on, and I see it is a fairly common issue - so is it something that happens when the file is being output by some poorly written Affymetrix software or why is it so common? I just can't think of any other time I have had a file go corrupt on me.
>
> Apologies if I am being naiive about file corruption in general.
>
> Thanks,
>
> Scott
>
>   -- output of sessionInfo():
>
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] hgu133plus2probe_2.12.0 hgu133plus2cdf_2.12.0   AnnotationDbi_1.22.6
> [4] simpleaffy_2.36.1       gcrma_2.32.0            genefilter_1.42.0
> [7] affy_1.38.1             Biobase_2.20.0          BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.28.0         annotate_1.38.0       BiocInstaller_1.10.2
>   [4] Biostrings_2.28.0     DBI_0.2-7             IRanges_1.18.1
>   [7] preprocessCore_1.22.0 RSQLite_0.11.4        splines_3.0.0
> [10] stats4_3.0.0          survival_2.37-4       tools_3.0.0
> [13] XML_3.98-1.1          xtable_1.7-1          zlibbioc_1.6.0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099