Question: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
5
gravatar for KJ Lim
5.3 years ago by
KJ Lim110
KJ Lim110 wrote:

Dear BioStar community,

Good day.

I have analyzed my RNA-Seq data with edgeR (R Bioconductor). The differential expression (DE) gene lists of my RNA-Seq data were obtained.

I would like to perform hierarchical clustering as well as heatmap analysis for the DE lists I obtained. I have been searching around for the right R packages or tools for these purposes as the RNA-Seq data is not same as microarray data.

Could the community kindly please light me where and how I should start?

Thank you very much. Have a nice day.

rna-seq heatmap • 21k views
ADD COMMENTlink written 5.3 years ago by KJ Lim110
7
gravatar for Obi Griffith
5.3 years ago by
Obi Griffith16k
Washington University, St Louis, USA
Obi Griffith16k wrote:

I don't think you necessarily need any special packages for doing clustering/heatmap analysis of RNAseq data versus microarray analysis. I've used heatmap.2 {gplots} for both. It has hierarchical clustering built in and you can easily specify different distance metrics and/or linkage criteria. You can start with your expression matrix, extract the subset for differentially expressed genes, and feed that into heatmap.2. If you search biostar for "heatmap" you will find all kinds of suggestions and tips on how to proceed as well as example code.

ADD COMMENTlink written 5.3 years ago by Obi Griffith16k

Thanks for the input :)

ADD REPLYlink written 5.3 years ago by KJ Lim110

Is there any particular wisdom to only selecting differentially expressed genes? It makes sense but I was wondering if this is only done because it is RNA-seq instead of a microarray, or maybe it was done with microarrays as well?

ADD REPLYlink written 17 months ago by cmdcolin700
5
gravatar for Nicolas Rosewick
5.3 years ago by
Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
Nicolas Rosewick6.0k wrote:

Check the DESeq package vignette (bioconductor) . There is a whole chapter on clustering RNA-seq data. http://bioconductor.org/packages/release/bioc/html/DESeq.html

ADD COMMENTlink written 5.3 years ago by Nicolas Rosewick6.0k

Dear Nicobxl, thanks for your suggestion. My RNA-Seq data already analyzed with edgeR, could it possible integrated in the DESeq package?

ADD REPLYlink written 5.3 years ago by KJ Lim110
1

DESeq used the same input as edgeR : a read count matrix. So yes it's very easy ;)

ADD REPLYlink written 5.3 years ago by Nicolas Rosewick6.0k
0
gravatar for Damian Kao
5.3 years ago by
Damian Kao14k
USA
Damian Kao14k wrote:

I wrote a post on this few weeks ago on how to do hierarchical clustering in scipy and displaying the results in a browser with javascript: http://blog.nextgenetics.net/?e=44

You can also adapt it to display the heatmap in R with ggplot2's tile plotting functions.

ADD COMMENTlink written 5.3 years ago by Damian Kao14k

pretty cool. would be nice if you could wrap that all in a function that would output the .js or fill and html template.

ADD REPLYlink written 5.3 years ago by brentp22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1406 users visited in the last hour