[BioC] affyPLM crashing R

Scott Robinson [guest] guest at bioconductor.org
Thu Dec 5 10:15:37 CET 2013

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,


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[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.

More information about the Bioconductor mailing list