[BioC] vsn2 bug?

[Wolfgang Huber]

Dear Tobias,

thank you. It would be helpful if you could provide me the file
resulting from
	save(til, file="til.rda")
via a download link. I will treat this confidentially if necessary.

 Best wishes
  Wolfgang

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


Straub ha scritto:
> 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
> ======================================================================
>