[BioC] vsn2 bug?

Wolfgang Huber huber at ebi.ac.uk
Wed May 30 18:36:57 CEST 2007

Dear Tobias,

it looks odd indeed, - can you provide me a reproducible script to
reproduce your problem? As Gordon pointed out earlier, I also need the
necessary input data (which does not need to be your data, but any sort
of data that reproduces your problem).

1. How does the "meanSdPlot" look for "old" and "new" ?

2. How the "pairs" plot of the 12 matrix columns against each other (see
man page of geneplotter::smoothScatter for an example how to make it)?

3. You can always use the old "vsn" function, in spite of the
deprecation warning it is still there as always and will remain so for a
while. Of course I hope this kind of problems can be sorted out with the
new implementation; working hard on it.

Thank you & Best wishes

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

 Straub ha scritto:
> Dear all,
> with the upgrade to bioc 1.5.0 I am facing vsn2.
> as already discussed in an older thread there are calculation  
> differences. however, in my dataset(s) I get a massive outlier  
> comparing the array means after normalization with old vsn and vsn2.
> scatterplot here: http://server7.pictiger.com/img/198354/other/vsn- 
> bioc.png
> my data are six replicates of dual color tiling microarray (193290  
> spots), i.e. i pass a 193290 x 12 matrix to vsn.
> i guess that's a bug, is it?
> Tobias
> ======================================================================
> Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
> tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany

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