[BioC] Error in xval: No Direct or Inherited Method for this call

[Martin Morgan]

Mike,

This is because the xval methods in MLInterfaces 1.4.0 expect exprSet
objects, whereas Golub_Merge et al are ExpressionSet.

The newest R (2.4.0) and latest Bioconductor (1.9.0) are just being
released. There the MLInterfaces functions are defined to use
ExpressionSet, and your code works. Either (a) use the 'deprecated'
exprSet golubMerge or (b) update R / Bioconductor / installed packages
and use ExpressionSet (which is meant as the replacement for exprSet,
and so the effort to update is the right long-term solution).

I'm not sure where the Golub_Merge crept in for you. My guess is that
you entered the input by hand, and 'corrected' for the deprecation
warning. A convenient way to run the examples is to just type

> example(xval)

Another possiblity is that the information about installed packages is
not transcribed correctly. Here the best practice is to cut and paste
the result of

> sessionInfo()

which for me says

sessionInfo()
Version 2.3.1 Patched (2006-06-20 r38364) 
x86_64-unknown-linux-gnu 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
  genefilter     survival   golubEsets MLInterfaces      Biobase 
    "1.10.1"       "2.24"      "1.2.4"      "1.4.0"     "1.10.1" 

With this configuration, example(xval) uses golubMerge and works as
advertised.

Martin

<mpg33 at drexel.edu> writes:

> I am tryibng to use xval to run KNNB on an exprSet object.  Trying
> to run down the source of my difficulties I went to the xval help
> file and executed the example shown below (also found in the xval
> help file).
>
>> library(golubEsets)
>> data(Golub_Merge)
>> smallG<-Golub_Merge[200:250,]
>> lk1<-xval(smallG, 'ALL.AML', knnB, xvalMethod='LOO', group=as.integer(0))
> Error in xval(smallG, "ALL.AML", knnB, xvalMethod = "LOO", group = as.integer(0)) : 
>         no direct or inherited method for function 'xval' for this call
>
>
> I am running R Version 2.3.1, and the attached packages are Biobase
> 1.10.1, MLInterfaces 1.4.0, and golubEsets 1.2.4.
>
> Following advice given for other instances of this error call I reinstalled the Biobase package using biocLite and ran the update.packages() function and replaced all the packages listed. 
>
> I am new to R and any help would be appreciated.  
>
> Thanks,
> Mike
>
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-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org