[BioC] interpretation of vsn normalized data

[Wolfgang Huber]

Hi Maurice,

in statistics it is sometimes useful to differentiate between (a) the 
estimator and (b) the true underlying quantity that you want to estimate.

For example, if you want to estimate the expectation value of a 
symmetric distribution, you can use the mean, or the median as 
estimators. They are both correct, but depending on the data they can 
provide different, and more or less appropriate answers.

With microarrays, (b) is the fold-change, that is the change in mRNA 
abundance. The log-ratio of fluorescence intensities is a simple and 
intuitive estimator for this, but if the fluorescence intensities become 
small, this estimator can have unpleasant properties, like large 
variance. The glog-ratio (what vsn provides) is an alternative 
estimator, which avoids the variance explosion, for the price of being 
biased towards 0 when the fluorescence intensities are small.

Note that the vsn function returns glog to base e (so a glog-ratio of 1 
corresponds to an estimated fold change of exp(1) = 2.718..) while many 
other packages use log2.

  Hope this helps
  Wolfgang




Maurice Melancon wrote:
> Hello All,
> 
> I used vsn to normalze my one-channel cDNA microarray experiment.  I'm sorry
> if this is an elementary question (I'm not a math person) but can vsn data
> be interpreted in similar fashion to log2 data, e.g. 1 log vale = 2-fold
> induction?  What would be the appropriate transformation to get to either
> log2 or raw data from vsn data?
> 
> Briefly, what I did was to normalize using vsn, then I used SAS to run
> anovas with pairwise comparisons and anova slicing.  Using the estimate
> function returns estimated differences between the reported means.  I am
> seeking then to bridge the gap between these estimates and actual fold
> changes.  I think this can be done, but I am unsure about how to either
> reverse-transform the vsn data or how to interpret it biologically (e.g. 1
> log = 2x fold change)
> 
> WIth thanks
> 
> Maurice
> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber