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

From: Kevin Wright <kwright68_at_gmail.com>
Date: Thu 16 Feb 2006 - 21:25:57 GMT

(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

R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Feb 17 09:07:30 2006

This archive was generated by hypermail 2.1.8 : Mon 20 Feb 2006 - 03:21:41 GMT