[R] heatmap scale parameter question

[Witold E Wolski]

I do not want to use the b word, but can anyone who also subscribes to
the r-developer list forward my observation regarding heatmap? I am
pretty confident that the behaviour of heatmap in R 3.0.1 is not that
one intended.




On 31 July 2013 14:03, Witold E Wolski <wewolski at gmail.com> wrote:
> Would anyone of the more experienced r-users explain to me the
> behaviour of the scale parameter in the heatmap function.
>
> different options for scale (R 3.0.1) do change only the colors but do
> not affect the dendrograms. Please see for yourself executing the
> following code:
>
> d <- matrix(rnorm(100),nrow=20)
> stats::heatmap(d)
> X11()
> heatmap(d,scale="column")
> X11()
> heatmap(d,scale="row")
> X11()
> heatmap(d,scale="none")
>
> In all four above cases the dendrograms look exactly the same
> However, scaling clearly affects clustering. see:
>
> d <- scale(d)
> heatmap(d,scale="none")
>
>
> best regards
>
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> ciao
>
> --
> Witold Eryk Wolski
>
>
> --
> Witold Eryk Wolski



-- 
Witold Eryk Wolski