[BioC] vsn with a reference set

[Wolfgang Huber]

Dear Roumyana

they are on the glog2 scale

   glog2(x) = log2( x + sqrt (x^2 + b^2) )

where b is of the order of the microarray background intensity, so glog2
is (up to a constant) the same as log2 for intensities well above
background, x>>b. The effect of the sqrt-term is similar to what is
called "background correction" in other approaches, namely to prevent
the argument of the log2 function to become zero or negative.

So you can treat the output of vsn2 like log2-transformed intensities,
their differences as log2-fold-changes, etc.

Best wishes
 Wolfgang

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


26/03/2008 17:11 Roumyana Yordanova a écrit
> 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