[BioC] vsn with a reference set

[Roumyana Yordanova]

Dear Wolfgang,

Thank you. My version of R was old and vsn2 did not work with AffyBatch 
objects.
However, when I run it with 2.6.2  I got very small numbers (also 
negative) for
x2 = exprs(justvsn(a2, ref=refvsn)). Are x2 the actual intensities or I 
need to process them further?

Roumyana

Wolfgang Huber wrote:

> Roumyana Yordanova wrote:
>
>> Dear Dr. Huber,
>>
>> I have a question regarding using vsn with a reference set.
>> I used it like this:
>>
>> ref <-ReadAffy(filenames=files.ref)
>> test <-ReadAffy(filenames=files.test)
>> ref.vsn <-justvsn(ref)
>> test.vsn <-justvsn(test,reference=ref.vsn)
>>
>> and got this error message
>> Error in vsnMatrix(m, reference, strata, optimpar = list(cvg.niter = 
>> 4L),: nrow(reference)' must be equal to 'nrow(x)'.
>>
>> I guess I am not using it right. Can you advise. Thank you very much.
>>
>> Sincerely,
>> Roumyana Yordanova
>
>
> Dear Roumyana
>
> you will need to generate a "vsn" object that contains the actual 
> model fit parameters, by using the function vsn2 on your object 'ref':
>
> You can then apply the model to the data in 'ref' by using 'predict', 
> and you can obtain a reference normalisation using vsn2 or justvsn 
> with the parameter 'ref' set. Please see the example below.
>
> Please also consider using the Bioconductor mailing list for this type 
> of questions!
>
>
> library("vsn")
> library("affydata")
>
> data("Dilution")
>
> a1 = Dilution[, 1:3]
> a2 = Dilution[, 4  ]
>
> refvsn = vsn2(a1)
> x1 = predict(refvsn, a1)
>
> x2 = justvsn(a2, ref=refvsn)
>
> x = justvsn(Dilution)
> par(mfrow=c(2,2))
> for(i in 1:4)
>   plot(exprs(x)[,i],
>        if(i<=3) exprs(x1)[,i] else exprs(x2)[,1],
>        pch=".")
>
>
>
>
> Best wishes
>   Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber