[BioC] affyPLM crashing R

Scott Robinson Scott.Robinson at glasgow.ac.uk
Sat Dec 7 12:11:24 CET 2013

Apologies, have found the mistake in my code - I had a number of affybatch objects floating around my script and had input the one with the NAs into fitPLM. Strange that it made R crash rather than just give me an error saying that it couldn't work with missing values.

I am now getting the error message:

Error in fitPLM(celFiles.HL) :
   INTEGER() can only be applied to a 'integer', not a 'NULL'

I thought perhaps I needed to round the numbers so they would fit an integer data type in whatever C library or whatever is being called here, but that didn't help.

Any ideas as to what is going on here?

-----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

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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