Unsupervised hierarchical clustering of DEG in Rstudio
Hi,
I want to perform unsupervised hierarchical clustering of DEG (output of edgeR) using Rstudio.
I found hclust and dist functions but not sure about which packages should I use.
I checked posts but that confused my mind more.
Could you please explain me the correct tools and methods for it?
• 2,842 views
•
link
updated
by
jared.andrews07
•
written
by
MS •
•
written
by
MS •
1 answer
You'll likely find the dittoSeq dittoHeatmap() function of interest. It can make heatmaps from your DGEList object directly for whatever genes you specify (and it's color blind-friendly by default).
• 0 views
•
link
written
by
jared.andrews07
Log in to answer this question.
More posts like this
-
Tutorial: Perform Hierarchical Clustering in R with ggdendro Visualization
written by Jeremy •
-
Tools for clustering genes rather than samples for bulk RNA-seq
written by ATS •
-
How to plot phylogenetic tree(dendrogram) of mitochondria haplogroups?
written by Karibu •
-
Hierarchical clustering using GISTIC 2.0 result
written by jhy •
-
Which is the proper RNA-seq count table transformation to perform hierarchial clustering analysis?
written by antonioggsousa
-
Beginners in Microarray analysis
written by mask2000 •
-
SC RNA genes clustering
written by moshe0110 •
-
Differentially expressed gene clustering
written by seta
-
Dealing With Probes With High Fold Change But Pa Call 0
written by gundalav
-
Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
written by KJ Lim •
What do you mean by "clustering of DEG"? Based on what? what would be the distance measure between DEGs?
Based on the expression profiles of differentially expressed genes obtained using EdgeR pakcage.
Maybe I'm missing something, but I still don't understand. Maybe if you elaborate on your experiment design and expected output, then I (or someone else) could help. In what case would you say two DEGs should be clustered together? Are you trying to perform some kind of co-expression analysis across conditions? Can you provide a link to a paper where this type on analysis was performed?
Sorry for the unclear explanation.
I have 2 groups as normal and patient and I have DEG list obtained with comparing these groups.
I just want to get heatmap showing expression profiles like the paper given the link below
http://cancerinflammation.dk/article/Diagnostic%20miRNA%20profiling%20in%20CTCL.pdf
No problem - got you now. So you want to cluster DEGs and samples. You need to create a matrix where the cell in row i and column j corresponds to the expression level for DEG i in sample j. Once you have that, I think this is what you need.