[BioC] Error with package ExpressionView

[Valerie Obenchain]

Hi Kavita,

It looks like this example is coming from the ExportEV man page.  All 
appears ok on this end if I load the package and run the example,

library(ExpressionView)
example("ExportEV")

If this is not the example you intended below please provide a small 
reproducible example and the output of your sessionInfo().

Valerie

Here is my sessionInfo(),

 > sessionInfo()
R Under development (unstable) (2011-11-27 r57757)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] hgu95av2.db_2.6.3    org.Hs.eg.db_2.6.4   ALL_1.4.11
  [4] eisa_1.7.0           genefilter_1.37.0    Category_2.21.0
  [7] isa2_0.3.1           ExpressionView_1.7.0 AnnotationDbi_1.17.5
[10] Biobase_2.15.2       BiocGenerics_0.1.3   RSQLite_0.10.0
[13] DBI_0.2-5            caTools_1.12         bitops_1.0-4.1

loaded via a namespace (and not attached):
  [1] GO.db_2.6.1      GSEABase_1.17.1  IRanges_1.13.13  KEGG.db_2.6.1
  [5] RBGL_1.31.1      XML_3.6-1        annotate_1.33.0  graph_1.33.0
  [9] splines_2.15.0   survival_2.36-10 tools_2.15.0     xtable_1.6-0


On 12/04/11 02:25, Kavita Garg [guest] wrote:
> I get an error while trying to run this from package "ExpressionView"
>
>
> ExportEV(by,y,filename = "file.evf",description = description)
>
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "annotation", for signature "matrix"
>
> Here:
> by = biclust object
> y = matrix
> description<- list( experiment=list(
> title="Title", xaxislabel="x-Axis Label",yaxislabel="y-Axis Label", name="Author", lab="Address", abstract="Abstract", url="URL", annotation="Annotation", organism="Organism"), coldata=coldata, rowdata=rowdata)
>
> Any suggestion would be great.
>
> thanks
> kavit
>
>   -- output of sessionInfo():
>
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] ALL_1.4.11           eisa_1.6.0           genefilter_1.36.0    Category_2.20.0      isa2_0.3.1           ExpressionView_1.6.0 AnnotationDbi_1.16.5
>   [8] Biobase_2.14.0       RSQLite_0.10.0       DBI_0.2-5            caTools_1.12         bitops_1.0-4.1       BiocInstaller_1.2.1  biclust_1.0.1
> [15] lattice_0.20-0       colorspace_1.1-0     MASS_7.3-16
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.32.0  GO.db_2.6.1      graph_1.32.0     GSEABase_1.16.0  IRanges_1.12.3   KEGG.db_2.6.1    RBGL_1.30.1      splines_2.14.0   survival_2.36-10
> [10] tools_2.14.0     XML_3.4-3        xtable_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