[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():
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_TIME=English_United Kingdom.1252
attached base packages:
 parallel stats graphics grDevices utils datasets methods
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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