[BioC] row.names in the latest vsn

[Roumyana Yordanova]

Dear Wolfgang,

Thanks a lot for your help.

Roumyana

Wolfgang Huber wrote:

> 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?
>>>
>>>
>>>  
>>>
>>
>>
>