[BioC] affyPLM crashing R

[Scott Robinson]

Dear Wolfgang,

I would have provided a reproducible example but even one of the CEL files alone is above my attachment size limit. Perhaps I could send you a short version of my R script and my Java program and you could try it on some CEL files of your own? Or maybe I could try sending a reproducible example through some kind of file transfer site like (after a Google around): www.wetransfer.com

I used Java to substitute the median in as R was too slow iterating over all 90 chips. I can only assume I was writing very inefficient code or else the Harshlight package was calling a C function rather than being written totally in R.

Thanks,

Scott


-----Original Message-----
From: Wolfgang Huber [mailto:whuber at embl.de] 
Sent: 05 December 2013 14:41
To: Scott Robinson [guest]
Cc: Bioconductor mailing list; Scott Robinson; affyPLM Maintainer
Subject: Re: [BioC] affyPLM crashing R

Dear Scott

Thank you. Can you provide a reproducible example? It is difficult to see how someone could follow up on your problem report without that.

	Kind regards
		Wolfgang



On 5 Dec 2013, at 10:15, Scott Robinson [guest] <guest at bioconductor.org> wrote:

> 
> I am trying to run affyPLM on an affybatch object and it has been crashing R.
> 
> When running it on my original affybatch object generated from "read.affy()" it works fine. I have been using Harshlight to substitute NAs into positions of spatial effects, then median scaling the chips together and replacing each NA with the median of the non-NA values at the same position on other chips.
> 
> It is with this new, spatially normalised, affybatch object that affyPLM is crashing R. Any ideas why?
> 
> Thanks in advance,
> 
> Scott
> 
> -- output of sessionInfo(): 
> 
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> 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] MASS_7.3-29           Harshlight_1.32.1     lattice_0.20-24      
> [4] corrplot_0.73         affyPLM_1.36.0        preprocessCore_1.22.0
> [7] simpleaffy_2.36.1     gcrma_2.32.0          genefilter_1.42.0    
> [10] affy_1.38.1           Biobase_2.20.1        BiocGenerics_0.6.0   
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.28.0        altcdfenvs_2.22.0    annotate_1.38.0     
> [4] AnnotationDbi_1.22.6 BiocInstaller_1.10.4 Biostrings_2.28.0   
> [7] DBI_0.2-7            graph_1.38.3         grid_3.0.2          
> [10] hypergraph_1.32.0    IRanges_1.18.4       makecdfenv_1.36.0   
> [13] RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2        
> [16] survival_2.37-4      tools_3.0.2          XML_3.98-1.1        
> [19] xtable_1.7-1         zlibbioc_1.6.0  
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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