[BioC] affyPLM crashing R
Scott.Robinson at glasgow.ac.uk
Thu Dec 5 17:43:00 CET 2013
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.
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
Thank you. Can you provide a reproducible example? It is difficult to see how someone could follow up on your problem report without that.
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,
> -- output of sessionInfo():
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>  LC_COLLATE=English_United Kingdom.1252
>  LC_CTYPE=English_United Kingdom.1252
>  LC_MONETARY=English_United Kingdom.1252
>  LC_NUMERIC=C
>  LC_TIME=English_United Kingdom.1252
> attached base packages:
>  parallel stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  MASS_7.3-29 Harshlight_1.32.1 lattice_0.20-24
>  corrplot_0.73 affyPLM_1.36.0 preprocessCore_1.22.0
>  simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0
>  affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0
> loaded via a namespace (and not attached):
>  affyio_1.28.0 altcdfenvs_2.22.0 annotate_1.38.0
>  AnnotationDbi_1.22.6 BiocInstaller_1.10.4 Biostrings_2.28.0
>  DBI_0.2-7 graph_1.38.3 grid_3.0.2
>  hypergraph_1.32.0 IRanges_1.18.4 makecdfenv_1.36.0
>  RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2
>  survival_2.37-4 tools_3.0.2 XML_3.98-1.1
>  xtable_1.7-1 zlibbioc_1.6.0
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