Search
Question: Unable to find an inherited method for function ‘exprs’
0
gravatar for Dave Tang
4.3 years ago by
Dave Tang210
Australia/Perth/TKI
Dave Tang210 wrote:
Hello, I'm getting this error when trying to use the exprs() function from the Biobase package: library(Biobase) exprs() Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?exprs? for signature ?"missing"? I was trying to use the virtualArray package, which required GEOquery, which required Biobase and the exprs() funciton. Cheers, -- Dave
ADD COMMENTlink modified 4.3 years ago by Wolfgang Huber13k • written 4.3 years ago by Dave Tang210
0
gravatar for Wolfgang Huber
4.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Dave this is actually not an error. The function 'exprs' expects and argument, and since you are giving it none, it complains, and one should not blame it for that. Perhaps can you tell us what you want to achieve, then it should be easier to help! Best wishes Wolfgang On 14 Aug 2013, at 05:08, Dave Tang <davetingpongtang at="" gmail.com=""> wrote: > Hello, > > I'm getting this error when trying to use the exprs() function from the Biobase package: > > library(Biobase) > exprs() > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?exprs? for signature ?"missing"? > > I was trying to use the virtualArray package, which required GEOquery, which required Biobase and the exprs() funciton. > > Cheers, > > > -- > Dave > > _______________________________________________ > 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 4.3 years ago by Wolfgang Huber13k
On Wed, 14 Aug 2013 12:13:31 +0900, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Dear Dave > this is actually not an error. The function 'exprs' expects and > argument, and since you are giving it none, it complains, and one should > not blame it for that. > Perhaps can you tell us what you want to achieve, then it should be > easier to help! Dear Wolfgang, Sorry for the incomplete email; I (incorrectly) thought there was a problem with the exprs() function and thus minimised the example. Here's the code following the virtualArray vignette: library("GEOquery") GSE13507 <- getGEO("GSE13507",GSEMatrix=FALSE, AnnotGPL=FALSE) summary(exprs(GSE13507)) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?exprs? for signature ?"GSE"? sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.26.2 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 tools_3.0.1 XML_3.98-1.1 Best, -- Dave
ADD REPLYlink written 4.3 years ago by Dave Tang210
Dear Dave have a look at the manual page of 'geoQuery', esp. the section titled "Value", and the package 'vignette'. They contain the answer to your question. I think many people have experienced that taking code examples that one saw somewhere and trying to tweak them to one's own problem by trial and error can be an efficient way to move forward; however, when it fails, it is a tradition on this mailing list to point out the existence of the more deductive approach of reading the software documentation and trying to understand what each component does. Best wishes Wolfgang On 14 Aug 2013, at 06:32, Dave Tang <davetingpongtang at="" gmail.com=""> wrote: > On Wed, 14 Aug 2013 12:13:31 +0900, Wolfgang Huber <whuber at="" embl.de=""> wrote: > >> Dear Dave >> this is actually not an error. The function 'exprs' expects and argument, and since you are giving it none, it complains, and one should not blame it for that. >> Perhaps can you tell us what you want to achieve, then it should be easier to help! > > Dear Wolfgang, > > Sorry for the incomplete email; I (incorrectly) thought there was a problem with the exprs() function and thus minimised the example. > > Here's the code following the virtualArray vignette: > > library("GEOquery") > GSE13507 <- getGEO("GSE13507",GSEMatrix=FALSE, AnnotGPL=FALSE) > summary(exprs(GSE13507)) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?exprs? for signature ?"GSE"? > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 > [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C > [5] LC_TIME=English_Australia.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GEOquery_2.26.2 Biobase_2.20.1 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 tools_3.0.1 XML_3.98-1.1 > > Best, > > > -- > Dave
ADD REPLYlink written 4.3 years ago by Wolfgang Huber13k
On Wed, 14 Aug 2013 13:48:42 +0900, Wolfgang Huber <whuber at="" embl.de=""> wrote: > I think many people have experienced that taking code examples that one > saw somewhere and trying to tweak them to one's own problem by trial and > error can be an efficient way to move forward; however, when it fails, > it is a tradition on this mailing list to point out the existence of the > more deductive approach of reading the software documentation and trying > to understand what each component does. Dear Wolfgang, I'll remember this next time before emailing too hasty. Thank you for the help and advice. Cheers, -- Dave
ADD REPLYlink written 4.3 years ago by Dave Tang210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 284 users visited in the last hour