[BioC] Error using normalize.AffyBatch.vsn()

[Wolfgang Huber]

Dear Markus,

thank you for point this out! The first problem you reported is now 
fixed in vsn_3.7.4 (soon here: 
http://www.bioconductor.org/packages/2.3/bioc/html/vsn.html)
This would have only affected very small AffyBatches (genechips with 
less than 30000 probes), but anyway the code now also deals properly 
with these.

The second problem: normalize.AffyBatch.vsn and the justvsn and vsn2 
methods for AffyBatch actually just make a copy of whatever object is 
given to them, modify the "exprs" slot, and return it. Hence the problem 
is with the "affybatch.example" dataset from the affy package. I cc its 
maintainer :)

Try with, e.g. the "Dilution" data from the affydata package, all should 
be fine.

	Best wishes
	Wolfgang



Markus Schmidberger a écrit 10/06/2008 15:42:
> Hello,
> 
> I get an error using "normalize.AffyBatch.vsn()"
> 
> Simple Testcode and sessionInfo():
> 
>  > data(affybatch.example)
>  > a <- affybatch.example
>  > normalize.AffyBatch.vsn(a)
> Fehler in validObject(.Object) :
>  invalid class "vsnInput" object: 'subsample' must be a numeric vector 
> of length 1 with values between 0 and 2400.
>  > sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
> locale:
> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  
> methods   base    other attached packages:
> [1] vsn_3.6.0            limma_2.14.4         affy_1.18.1          
> preprocessCore_1.2.0 affyio_1.8.0       [6] Biobase_2.0.1        
> lattice_0.17-6     loaded via a namespace (and not attached):
> [1] grid_2.7.0
> 
> ##################################################
> 
> I think the predefined subsample is to big ( subsample = 30000L  ->  
> subsample = 0L )
> If I define a smaller subsample, then it works. But I get a wrong 
> AffyBatch!
> 
>  > normalize.AffyBatch.vsn(a, subsample=1000)
> vsn: 2400 x 3 matrix (1 stratum).   0% done.
> 14% done.
> 28% done.
> 42% done.
> 57% done.
> 71% done.
> 85% done.
> 100% done.
> Please use 'meanSdPlot' to verify the fit.
> AffyBatch out-of-date; consider 'updateObject(<AffyBatch>)'
> AffyBatch object
> size of arrays=100x100 features (27 kb)
> cdf=cdfenv.example (150 affyids)
> number of samples=3
> number of genes=150
> annotation=
> notes=
> 
> ######################################
> 
> If I use justvsn(), it works. But again, I will get a WRONG AffyBatch!
> 
>  > justvsn(a)
> vsn: 10000 x 3 matrix (1 stratum).   0% done.
> 25% done.
> 50% done.
> 75% done.
> 100% done.
> Please use 'meanSdPlot' to verify the fit.
> AffyBatch out-of-date; consider 'updateObject(<AffyBatch>)'
> AffyBatch object
> size of arrays=100x100 features (7 kb)
> cdf=cdfenv.example (150 affyids)
> number of samples=3
> number of genes=150
> annotation=
> notes=
> Do I have to think about this warning?
> 
> Thanks
> Markus
> 

-- 
Best wishes
  Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber