Question: DESeq estimateDispersions() problem
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gravatar for delhomme@embl.de
6.9 years ago by
delhomme@embl.de1.2k wrote:
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 • 1.1k views
ADD COMMENTlink modified 6.9 years ago by Steve Lianoglou12k • written 6.9 years ago by delhomme@embl.de1.2k
Answer: DESeq estimateDispersions() problem
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gravatar for Steve Lianoglou
6.9 years ago by
Denali
Steve Lianoglou12k 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
ADD COMMENTlink written 6.9 years ago by Steve Lianoglou12k
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 REPLYlink written 6.9 years ago by delhomme@embl.de1.2k
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 REPLYlink written 6.9 years ago by Karl Lundén20
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