DESeq estimateDispersions() problem

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delhomme@embl.de ★ 1.2k

@delhommeemblde-3232

Last seen 9.7 years ago

Dear Karl, Can you please paste in your session info as well, that will help the maintainer. To get it use the sessionInfo command in R after having loaded the DESeq package. I would not expect such a function to disappear without being deprecated, but you can always lookup the package recent changes using the news command: news(package="DESeq") Depending on your R version, you can query more specific new, i.e. if you're using the current development version: news(Version >= "1.9", package="DESeq") As I said, since I do not expect such a drastic change in the DESeq API, make sure as well that nothing changed in your R environment: check that no previous session is restored when you start R (look for an .Rdata file in the startup directory), etc. Cheers, --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On May 31, 2012, at 2:29 PM, Karl Lund?n wrote: > Dear all, > I can not get the DESeq function estimateDispersions() to function as it usually > does. Have there been any recent updates in DESeq or in R that explains why > estimateDispersions doesn't work? I use R on a grid engine and everything worked > fine earlier this spring. > Thanks > Karl > ================================================ >> library(DESeq) >> ?newCountDataSet() >> library(DESeq) >> ?estimateDispersions() > Error in .helpForCall(topicExpr, parent.frame()) : > no methods for 'estimateDispersions' and no documentation for it as a function >> estimateDispersions() > Error: could not find function "estimateDispersions" > > ## Other functions do work >> newCountDataSet() > Error in as.matrix(countData) : > argument "countData" is missing, with no default > > _______________________________________________ > 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

DESeq DESeq • 2.1k views

ADD COMMENT • link updated 11.9 years ago by Steve Lianoglou ★ 13k • written 11.9 years ago by delhomme@embl.de ★ 1.2k

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 14 months ago

United States

Hi Karl, estimateDispersions is still definitely there ... you can verify that by looking through the the DESeq Reference Manual: http://bioconductor.org/packages/2.10/bioc/manuals/DESeq/man/DESeq.pdf It seems there's something wonky going on with your install. As Nicolas said, providing the output from `sessionInfo()` after you load DESeq will be most helpful. As a side note, I just want to point out that you are trying to invoke the help incorrectly: On Thu, May 31, 2012 at 8:29 AM, Karl Lund?n <karl.lunden at="" slu.se=""> wrote: [snip] >> library(DESeq) >> ?estimateDispersions() > Error in .helpForCall(topicExpr, parent.frame()) : > ?no methods for 'estimateDispersions' and no documentation for it as a function You should remove the open/close parens. So your call to help should be: R> ?estimateDispersions HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 11.9 years ago Steve Lianoglou ★ 13k

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Indeed; good catch Steve. Calling the help that way gives me a very similar error to the one you reported: ?estimateDispersions() Error in .helpForCall(topicExpr, parent.frame()) : no documentation for function ?estimateDispersions? and signature ?object = "ANY"? In addition: Warning message: In .helpForCall(topicExpr, parent.frame()) : no method defined for function ?estimateDispersions? and signature ?object = "ANY"? whereas this works as expected: ?estimateDispersions Help on topic ?estimateDispersions? was found in the following packages: Package Library DESeq /Library/Frameworks/R.framework/Versions/2.15/Resources/library Biobase /Library/Frameworks/R.framework/Versions/2.15/Resources/library <truncated output=""> >sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq_1.8.2 locfit_1.5-8 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.0 DBI_0.2-5 IRanges_1.14.3 [4] RColorBrewer_1.0-5 RSQLite_0.11.1 annotate_1.34.0 [7] genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0 [10] lattice_0.20-6 splines_2.15.0 stats4_2.15.0 [13] survival_2.36-14 xtable_1.7-0 Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Jun 1, 2012, at 4:06 PM, Steve Lianoglou wrote: > Hi Karl, > > estimateDispersions is still definitely there ... you can verify that > by looking through the the DESeq Reference Manual: > > http://bioconductor.org/packages/2.10/bioc/manuals/DESeq/man/DESeq.pdf > > It seems there's something wonky going on with your install. As > Nicolas said, providing the output from `sessionInfo()` after you load > DESeq will be most helpful. > > As a side note, I just want to point out that you are trying to invoke > the help incorrectly: > > On Thu, May 31, 2012 at 8:29 AM, Karl Lund?n <karl.lunden at="" slu.se=""> wrote: > [snip] >>> library(DESeq) >>> ?estimateDispersions() >> Error in .helpForCall(topicExpr, parent.frame()) : >> no methods for 'estimateDispersions' and no documentation for it as a function > > You should remove the open/close parens. So your call to help should be: > > R> ?estimateDispersions > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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 REPLY • link 11.9 years ago delhomme@embl.de ★ 1.2k

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Thanks! I am working on the reinstallation. Karl Jun 1, 2012 kl. 4:33 PM skrev Nicolas Delhomme: > Indeed; good catch Steve. Calling the help that way gives me a very similar error to the one you reported: > > ?estimateDispersions() > Error in .helpForCall(topicExpr, parent.frame()) : > no documentation for function ?estimateDispersions? and signature ?object = "ANY"? > In addition: Warning message: > In .helpForCall(topicExpr, parent.frame()) : > no method defined for function ?estimateDispersions? and signature ?object = "ANY"? > > whereas this works as expected: > > ?estimateDispersions > Help on topic ?estimateDispersions? was found in the following > packages: > > Package Library > DESeq /Library/Frameworks/R.framework/Versions/2.15/Resources/library > Biobase /Library/Frameworks/R.framework/Versions/2.15/Resources/library > <truncated output=""> > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DESeq_1.8.2 locfit_1.5-8 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.0 DBI_0.2-5 IRanges_1.14.3 > [4] RColorBrewer_1.0-5 RSQLite_0.11.1 annotate_1.34.0 > [7] genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0 > [10] lattice_0.20-6 splines_2.15.0 stats4_2.15.0 > [13] survival_2.36-14 xtable_1.7-0 > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme at embl.de > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > > On Jun 1, 2012, at 4:06 PM, Steve Lianoglou wrote: > >> Hi Karl, >> >> estimateDispersions is still definitely there ... you can verify that >> by looking through the the DESeq Reference Manual: >> >> http://bioconductor.org/packages/2.10/bioc/manuals/DESeq/man/DESeq.pdf >> >> It seems there's something wonky going on with your install. As >> Nicolas said, providing the output from `sessionInfo()` after you load >> DESeq will be most helpful. >> >> As a side note, I just want to point out that you are trying to invoke >> the help incorrectly: >> >> On Thu, May 31, 2012 at 8:29 AM, Karl Lund?n <karl.lunden at="" slu.se=""> wrote: >> [snip] >>>> library(DESeq) >>>> ?estimateDispersions() >>> Error in .helpForCall(topicExpr, parent.frame()) : >>> no methods for 'estimateDispersions' and no documentation for it as a function >> >> You should remove the open/close parens. So your call to help should be: >> >> R> ?estimateDispersions >> >> HTH, >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> 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 REPLY • link 11.9 years ago Karl Lundén ▴ 20

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