[BioC] Confusing colours using geneplotter functions and heatmap()

[michael watson (IAH-C)]

Hi

I am using heatmap() to create a heatmap (obviously) and using the
function:

greenred.colors()

To create a list of green/red colors to use.  However, the results are
very confusing!

My spot ME7_823 has a value of -0.4 for a particular column, another
spot NB_774D has a value of -0.6 and a third spot ME7_949 a value of
-0.7.  :

ME7_823	-0.4
NB_774D	-0.6
ME7_949	-0.7

Now, I would expect all of these values to be green, and for ME7_949 to
be brighter than NB_774D which in turn would be brighter than ME7_823,
which would be the darkest as it is the lowest value.  THIS IS NOT THE
CASE!  In my heatmap(), NB_774D is clearly the darkest, then ME7_823 and
then ME7_949 is the brightest.

Clearly this is not how it should be, UNLESS heatmap() only assigns
colours relative to each row individually, and does not do any
comparison between rows.  Is this the case?  Won't this lead to
misleading results?  Surely the colour assigned to a spot in a heatmap
should reflect that spot's "position" in the whole dataset, not just the
data for that row of the matrix?  If the latter is true, then values of
5000 and 0.5 could be assigned the same colour, simply because they are
in the same position relative to their respective genes - and that would
render making comparisons vertically in a heatmap() useless...?

Cheers
Mick