[BioC] vsn on log2 transformed data?

[James W. MacDonald]

Hi Kamila,

Kamila Naxerova wrote:
> Hi!
> 
> Could anyone explain to me *why* I cannot apply vsn to log2 transformed 
> data? "...may not satisfy the requirements of the 
> multiplicative-additive noise model" is a little hard to grasp for 
> someone without a rigorous statistical background and the vignette and 
> the original publication did not enlighten me very much. Does this 
> really mean I cannot use vsn on a data set that contains log2 
> transformed ratios from a dual channel experiment?

One of the reasons people log transform their microarray data is to 
decrease (or eliminate) the dependence between the mean and variance. In 
other words, with un-logged data, the variance between samples will tend 
to change depending on the intensity of the spot. Many statistical tests 
assume independence between the mean and variance, so we want to 
minimize the dependence as best as possible.

vsn is also designed eliminate the dependence between the mean and 
variance. It makes different assumptions about the structure of the 
dependence (the multiplicative-additive noise model you mention above), 
but in the end the goal is the same as taking logs.

Now, if you have log2 transformed data, you have _already_ done 
something to eliminate the mean-variance dependence. These data most 
likely won't "satisfy the requirements of the multiplicative-additive 
noise model", because that model assumes the data are on the original 
scale, and that the variance is still dependent on the mean. Since this 
is not true, you may not get reasonable results, and it is really not 
necessary.

Long story short, if you want to use vsn on your data, you need to start 
with the background-corrected un-logged cy3 and cy5 intensity values.

Does that help?

Best,

Jim


> 
> Thanks for any help!!!
> Kamila
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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