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

From: Earl F. Glynn <>
Date: Fri 17 Feb 2006 - 19:34:15 GMT

"Kevin Wright" <> wrote in message
> (I have searched the email archives for discussions on this topic but
> have found nothing.)
> 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?
. . .
> 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.

I second this recommendation for exactly the same reasons. Last week I spent an hour or so trying to figure out why the heatmap colors for the same number were different across several related heatmaps. Turning the scaling off removed the surprise color differences. I will always want scale="none" as my default and now must remember to always specify it.

If the default is not changed, I think a WARNING should be included in the documentation about this.

efg mailing list Received on Sat Feb 18 06:37:23 2006

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