[BioC] Does old workspace work?

[Robert Gentleman]

Hi,

Loren Engrav wrote:
>> sessionInfo()
> R version 2.8.0 Patched (2008-10-26 r46783)
> i386-apple-darwin9.5.0
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> methods   base     
> 
> other attached packages:
> [1] simpleaffy_2.18.0  genefilter_1.22.0  survival_2.34-1    affyio_1.10.0
> porcinecdf_2.3.0   gcrma_2.14.0       matchprobes_1.14.0 affy_1.20.0
> Biobase_2.2.0     
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.4.0  DBI_0.2-4            RSQLite_0.7-1
> annotate_1.20.0      preprocessCore_1.4.0
> 
> ==============
> A year or so ago I ran 64bit R on Mac PPC and saved various workspaces
> 
> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5
> 
> I load up the old workspaces
> and I enter
> 
>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt")
> Where ABeset_gcrma is an old file
> 
> and I get
> Error in function (classes, fdef, mtable)  :
> unable to find an inherited method for function "write.exprs", for signature
> "exprSet"
> 
   It was probably more than a year ago - the exprSet class was 
deprecated and subsequently made defunct.

   You could try to do:
  library(Biobase)

   updateObject(ABeset_gcrma)

  failing that, you can try something like
   write.table(ABeset_gcrma at exprs, 
file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t",
         col.names = NA)

  or something like that.

> And I enter
>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv")
> 
> And I get
> Error: could not find function "exprs2excel"

   That function has been made defunct.
> 
> Am I doing something wrong?

   No, you just can't expect that things won't change.

  best wishes
    Robert

> 
> Thank you
> 
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org