[BioC] simple

[Scott Robinson]

Thanks James and Kasper, I will try redownloading and if that fails then getting in contact with the group that orginally gathered the data.

Kind Regards,

Scott
________________________________________
From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com]
Sent: 11 July 2013 16:04
To: James W. MacDonald
Cc: Scott Robinson [guest]; bioconductor at r-project.org; Scott Robinson
Subject: Re: [BioC] simple

In my experience this sometimes happens when you download a large batch of arrays (typically from some repository) and there is some corruption in one of the files, which happens occasionally when downloading from public repositories. I tend to just re-download the corrupted file.

The alternative is that the files are output by some software not adhering to the file format specification, but that is only an issue if you know people could have been tampering with the file. In this case you would expect most of the files to be corrupted.

Best.
Kasper


On Thu, Jul 11, 2013 at 9:58 AM, James W. MacDonald <jmacdon at uw.edu<mailto:jmacdon at uw.edu>> wrote:
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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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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