[R] One question on heatmap

[Peter Langfelder]

Before plotting a heatmap we usually standardize all genes to mean
zero and variance 1. That way the green/red represent under/over
expression with respect to the mean expression, which is roughly what
the original 2-color arrays (that literally produced such heatmaps)
were measuring. Of course, standardization assumes you have more than
2 samples.

If your expression matrix is stored in the variable expr, with columns
corresponding to samples and rows to genes, you can obtain a
standardized expression matrix as

stdExpr = t(scale(t(expr)))


Peter


On Tue, Nov 2, 2010 at 8:50 AM, Hua <kaixinsjtu at gmail.com> wrote:
> Dear R-helper:
>
> Suppose we have a matrix:
>
> Gene            sample1 sample2
>
> Gcnt1            12.0000    52.80000
> Max               8.8000    39.10000
> Tmem176b         67.9000   304.70000
> Shmt2             8.6000    42.40000
> Rtn4             11.5000    57.70000
> Il17re            7.6000    38.80000
> Bclp2             6.2000    32.10000
> Mobkl3            4.4000    32.20000
> Akr1b10           3.4000    30.10000
> Atp6ap2           5.4000    48.20000
> Snx2              5.7000    63.10000
> Tmem176a          7.6000    91.40000
> Klhl9             1.7000    30.30000
> Fbxo27            1.0000    28.90000
> Scd1             34.6000     0.70000
> Tspan9           35.8000     4.20000
> 2210016L21Rik    39.1000     4.90000
> Ctnnb1          212.1000    33.10000
> Apoe            397.2000    74.20000
> H2-DMb1          72.3000    14.10000
> Ryk              31.7000     6.40000
> Dapk2            85.4000    17.30000
> Gzmm            179.4000    36.80000
> Actb          12993.4000  2678.10000
> Faim3           758.0000   157.60000
> Aktip           209.4000    46.00000
> Tbrg1            93.3000    21.30000
>
> When I try to make heatmap based on this gene expression value table, I found that, when I set 'scale' to 'column', the heatmap will be always be red. I think this is because, there's very large values in the matrix (gene Actb), while the most are just very small. Thus, the color will be very ugly. I just wonder, how to set the color to make the heatmap look better?  I have tried log-tranformation on the matrix and it's better now. But I do want to know if you have better ways to set the color span manually and make the heatmap look better without any log-transformation?
>
> Thanks in advance!
>
> Best, Hua
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