[BioC] Unable to find an inherited method for function ‘exprs’

[Wolfgang Huber]

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