[BioC] Bug fix to made4

Aedin Culhane aedin at jimmy.harvard.edu
Sun Jun 17 17:31:21 CEST 2007

Dear Made4 users,
There was a bug in heatplot in made4 v1.10.  The default color scheme
of the heatmap had the colors "reversed".

As this is potentially confusing to users, I have corrected this bug in
Bioconductor and the version number is incremented to 1.10.1

Now down-regulated genes are blue (cold color) and up-regulated genes
are red/brown (warm colors).

heatplot() does "Eisen" hierarchical cluster analysis, in that it uses
1-Pearson Correlation as the default distance and average linkage as the
default joining method.

I had implmented a new color scheme in version 1.10. The previous
Version 1.9 used a red-green color scheme, but in v1.10 heatplot uses
the color scheme of red/brown - blue as defined in Colors defined by
Huber, Li & Gentleman, Chapter 10, Bioinformatics & Computational
Biology Solutions using R & Bioconductor (2006). You can of course,
still use the old scheme, by setting cols.default=FALSE.


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