How can I interpret heat maps and Principale component analysis?
In the assignment I am doing we have two genotypes B and b. the assembly has two scaffolds and the aim is to test whether any part of the assembly is associated with B or b variants. And so we created heat maps and ran PCA on the genotypes. So we are suppose to analyse it and give summary statistics or a plot describing the patterns of differentiation.
Can any one please help me understand how to? I have never done it and am not familiar with it.
• 6,417 views
•
link
written
by
oshin707 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Polygenic risk scores in a twin sample
written by juanjose.madridvalero •
-
Mapping an assembled genome to a sex chromosome
written by Lilnet •
-
Heatmap using Interaction/HiCHip data
written by pixie@bioinfo
-
TSS centered heatmap using Interaction/HiCHip data
written by pixie@bioinfo
-
Find chromosomal location of a scaffold
written by Jautis
-
Claiming two association signals are independent if only summary statistics and reference LD are av…
written by LauferVA
-
plotting with python
written by oshin707 •
-
Heat map generation
written by tanni93 •
-
Investigating a genome assembly
written by thjnant
-
How Can I Create A Heat Map With Phylogeny In R?
written by microbeatic
Some theory first:
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap
http://nar.oxfordjournals.org/content/early/2015/05/12/nar.gkv468.full
The authors write about interpretation of both.
and this one:
http://biorxiv.org/content/biorxiv/early/2016/09/21/076463.full.pdf
shinyheatmap: ultra fast low memory heatmap software for big data genomics
thank you so much for the links
For PCA reading this question (and the answers) in CV may help. Currently, is the top question by votes raking!.