[BioC] row.names in the latest vsn

[Wolfgang Huber]

Dear Roumyana,

this is because I rationalized the function structure, as follows:

1.) The generic function "vsn2" has methods for data objects of class 
AffyBatch, ExpressionSet, NChannelSet, RGList and matrix. It returns a 
fit object of class "vsn" with model fit parameters etc. The generic 
function "predict" applies a fitted model to a data object (of any of 
the above classes) and, in the case of AffyBatch and in most other 
cases, returns a data object of the same class and shape.

2.) So "justvsn" is now literally just as follows:

justvsn = function(x,  ...) {
     fit = vsn2(x, ...)
     predict(fit, newdata=x, useDataInFit=TRUE)
   }

3.) If you also want to do the probe-set summarization by RMA (an 
Affymetrix-specific feature that has nothing directly to do with vsn), 
you can call

   vsnrma

which is a wrapper around "justvsn" and then "rma" from the affy package 
where the latter is called with options normalize=FALSE, background=FALSE.

Bottomline: please have a look at the vsnrma function.

Also, for all those of you who have endured the vsn version 1 --> 
version 2 transition, to all intents and purposes the reengineering of 
vsn is now done and I intend to make no further changes to the user 
interface.

Best wishes
   Wolfgang

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

Roumyana Yordanova wrote:
> Dear Wolfgang,
> 
> It seems that justvsn in the last version 
> (http://www.bioconductor.org/packages/devel/bioc/html/vsn.html) does not 
> output the row.names (the corresponding probe sets names). Can this be 
> something related to changes in the AffyBatch object?
> 
> Roumyana
> 
> Roumyana Yordanova wrote:
> 
>> Dear Wolfgang,
>> Thanks for your help. For anyone that applies vsn2 to AffyBatch 
>> objects with a reference set please use the last version of vsn 
>> http://www.bioconductor.org/packages/devel/bioc/html/vsn.html
>> Roumyana
>>  
>>
>>
>> ------------------------------------------------------------------------
>>
>> Subject:
>> Re: vsn with a reference set
>> From:
>> Wolfgang Huber <huber at ebi.ac.uk>
>> Date:
>> Fri, 28 Mar 2008 12:05:40 +0000
>> To:
>> Roumyana Yordanova <roumyana.yordanova at bms.com>
>>
>> To:
>> Roumyana Yordanova <roumyana.yordanova at bms.com>
>>
>>
>> 28/03/2008 04:55 Roumyana Yordanova a écrit
>>  
>>
>>> Dear Wolfgang,
>>> Thanks a lot. I got the current version and it works.
>>> Roumyana
>>>
>>>   
>>
>> Dear Roumyana
>>
>> thank you! Could you post this reply to the mailing list, so that
>> everybody knows that they should upgrade their vsn if they want to work
>> with reference normalisation and AffyBatch objects?
>>
>>
>>  
>>
> 
>