[BioC] Confusing colours using geneplotter functions and heat map()

[Liaw, Andy]

?heatmap says, under `Argument':

   scale: character indicating if the values should be centered and
          scaled in either the row direction or the column direction,
          or none.  The default is '"row"' if 'symm' false, and
          '"none"' otherwise.

and the default is `row'.  I guess you know what to do from here...

Andy

> From: 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
> 
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