[BioC] interpretation of vsn normalized data
Wolfgang Huber
huber at ebi.ac.uk
Thu Feb 16 19:16:24 CET 2006
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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>
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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
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