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

[Markus Schmidberger]

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AffyBatch out-of-date; consider 'updateObject(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AffyBatch out-of-date; consider 'updateObject(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

-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599