From kwright68 at gmail.com  Thu Feb 16 22:25:57 2006
From: kwright68 at gmail.com (Kevin Wright)
Date: Thu, 16 Feb 2006 15:25:57 -0600
Subject: [Rd] Could heatmap default to scale="none" ?
Message-ID: <adf71a630602161325p17a92220p4774012ac5e7a33d@mail.gmail.com>

(I have searched the email archives for discussions on this topic but
have found nothing.)

The help page for heatmap says:
By default (scale = "row") the rows are scaled to have mean zero and
standard deviation one. There is some empirical evidence from genomic
plotting that this is useful.

I offer two comments on that.

1. Since the heatmap function is general-purpose (that is, not in a
genomics package), wouldn't it be better to just use no scaling?

2. Why assume that the rows should be scaled instead of the columns? 
There appears to be an assumption on the structure of the data.  Is
this assumption really warranted for a general-purpose function?

For the data I'm analyzing, scaling has hidden a great deal of
structure and I've just had to re-do many hours of work because I
didn't thoroughly read the help page and was not expecting the
scaling.  Further, given the structure of my data I did try (manually)
centering (not scaling) the COLUMNS, not the rows.

The heatmap.2 function in the gplots package defaults to scale="none"
and I argue that it would be better for the heatmap function to do the
same.

Kevin Wright



[Rd] Could heatmap default to scale="none" ?
Kevin Wright