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 <kaixins...@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 > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
