[BioC] vsn2 bug?

[Tobias Straub]

Dear Wolfgang,

this is how I run vsn:

#####################################
library(vsn)

#get the matrix of raw intensities
d.raw <- as.matrix(til[,5:16])

d.norm.old <- vsn(d.raw, subsample=20000)
d.norm.new <- vsn2(d.raw, subsample=20000)

#####################################

I just discovered, that if I don't use subsampling the poblem gets  
even worse:
http://www.badongo.com/pic/689985

the meanSdPlot (with subsampling) looks like this:
http://www.badongo.com/pic/690005

the pairs of my matrix (pre-vsn) looks like this:
http://www.badongo.com/pic/690007

If you want I can provide you the complete dataset via a local  
download link.

best wishes
Tobias

On May 30, 2007, at 6:36 PM, Wolfgang Huber wrote:

>
> 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
>
> ------------------------------------------------------------------
> 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
>>

======================================================================
Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany