Question: affyPLM crashing R
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5.9 years ago by
Guest User12k
Guest User12k 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.
affyplm harshlight • 625 views
ADD COMMENTlink modified 5.9 years ago by Wolfgang Huber13k • written 5.9 years ago by Guest User12k
Answer: affyPLM crashing R
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gravatar for Wolfgang Huber
5.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.9 years ago by Wolfgang Huber13k
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@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.9 years ago by Scott Robinson130
Never mind that last e-mail, it will be small enough zipped. Just wasn't thinking. I will make a small example tomorrow and reply again. Many thanks, Scott -----Original Message----- From: Wolfgang Huber [mailto:whuber@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.9 years ago by Scott Robinson130
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@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 5.9 years ago by Scott Robinson130
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