[BioC] simple

[Scott Robinson [guest]]

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."

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   

--
Sent via the guest posting facility at bioconductor.org.