How to make a heatmap in R for a microarray data?

#1
Hi guys,

I have been given a microarray data for which I need to figure out a heatmap. Unfortunately I have never had a chance and experience in this field. I even don't know how to use the R. Recently I try to learn the R and I have know how to read the data into the system. Could someone please tell me which program I can use to draw the heatmap?

Here is the data format saved in my computer:
_____________________________________________________
obs Exposure Gender Gene1 Gene2 Gene3 ........ Gene1503
1 1 1 0.543 0.187 0.856 ........ 0.425
2 0 1 ...
3 1 0 ...
...
50 1 1 .... ....

Please note: all the genes' value are larger than or equal to 0 and less than or equal to 1.

I am not fimiliar with the syntax of R. So, if you would like to contribute you answer to this post, please wirte the sentence in detail.

Thank you very much!
 
Last edited:

mp83

TS Contributor
#2
Take a look at this. I think it is well documented for you.

Using R to draw a Heatmap from Microarray Data

The first section of this page uses R to analyse an Acute lymphocytic leukemia (ALL) microarray dataset, producing a heatmap (with dendrograms) of genes differentially expressed between two types of leukemia.
There is a follow on page dealing with how to do this from Python using RPy.
The original citation for the raw data is "Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival" by Chiaretti et al. Blood 2004. (PMID: 14684422)
The analysis is a "step by step" recipe based on this paper, Bioconductor: open software development for computational biology and bioinformatics, Gentleman et al. 2004. (...)
> http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/heatmap/#R