[BioC] Heatmap hints and identifying differentially expressed genes

Marietta Herrmann mariherrmann at gmx.de
Mon Mar 2 16:10:14 CET 2009

Hi Amy,

you can set up every color you want with this command:

mycolors<-function(n) colorpanel(n, "blue", "white", "brown")

you can fit in every color from the R color chart, which you can find here:

in the heatmap-command you set col=mycolors(32)

I hope this helps you!

Best regards,

Marietta Herrmann

Am 3/2/09 3:34 PM schrieb "Amy Johnson" unter <a7johnson at gmail.com>:

> Hi,
> I'm new to biostatistics and R programming. I need some help for heatmap or
> heatmap.2 functions, especially I'm confused about the color settings.
> Here is what I'm trying to do: I have microarray data with several groups
> of treated samples and one group of control samples. I have calculated
> the averaged intensity of each gene in each group and calculated the
> simple fold change by comparing it to corresponding gene in the control
> group. I have picked the activated genes (>2-fold) and repressed genes
> (<0.5-fold). Now I need to show my boss of the fold changes in heatmap.
> I'd like to shown genes with fold changes < 1 in blue gradient color and
> genes with fold changes > 1 in red gradient color. Genes with
> fold-changes close to 1 in yellow color. How do I specify the color
> parameter in heatmap (or heatmap.2) function?
> Heat is my code (not working):
> data <- read.csv("mydata.csv", header=TRUE);
> library(gplots);
> x <- as.matrix(data);
> heatmap.2(x, Rowv=FALSE, Colv=FALSE, col=rev(redgreen(100)), key=FALSE,
> trace="none", dendrogram="none");
> mydata.csv is like this:
> treat1,treat2,treat3
> GREB1,9.3,6.47,5.37
> SUSD3,7.95,3.41,3.64
> FOS,6.68,15.91,18.02
> GAL,3.63,1.19,1.33
> CXCL12,3.58,2.59,2.24
> SLC7A5,3.52,2.1,3.24
> LOC51057,3.45,0.83,2.53
> PKIB,3.45,0.79,0.8
> H2-ALPHA,3.38,2.57,2.22
> LRRC54,3.25,7.11,5.04
> ...
> LOC57400,0.31,0.67,0.23
> ABCC3,0.3,0.47,0.4
> BX118285,0.3,0.59,0.37
> AY227436,0.29,0.4,0.14
> AF222023,0.29,0.53,0.27
> FLJ20489,0.26,0.62,0.28
> FHL5,0.26,0.29,0.28
> AB014766,0.24,0.38,0.22
> Note that, I need heatmap to be in color blue-yellow-red, but I have no
> idea how to specify that. Any help will be appreciated.
> Here is another quick question: how do I calculate the p-value for each
> gene? I'm simply calculating the fold-changes. But it is better to do
> some kinds of statistical analysis. In my experiment, each sample group
> is in triplicate. What is the best way to pick up differentially
> expressed genes (not using fold changes)?
> Thanks in advance.
> Amy
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