Hierarchical Clustering: DENDROGRAMS - what are they, and how are they used?

Hierarchical clustering is an agglomerative clustering technique summarised using a dendrogram. This video will look at how the algorithm works, and how information is conveyed using a dendrogram. Finally, you'll see how to work with dendrograms using JMP Software.
Content Index:
00:00 Introduction
00:26 Hierarchical Clustering
01:32 Dendrogram Diagram
03:44 Dendrograms using JMP Software
05:32 Conclusion

[@biancamangion7750]

Thank you for helping me understand dendrograms!

[@PegaAnalytics]

Happy to hear the video helped :)

[@jupjup2023]

Thanks for the great video! It would be very appreciated if you will discuss how to select the optimum number of clusters in future videos. 🙂

[@PegaAnalytics]

I appreciate your feedback. I'll make a note to make a video about identifying the optimal number of clusters - thanks for the suggestion.

[@rlwsu]

Thank you very much great video.

[@PegaAnalytics]

I'm glad you liked it. I appreciate the feedback. Thanks!

[@Helenalovedog]

Thank you for the wonderful video! I had a very vague understanding of this concept before watching it. However, after going through the video, everything became crystal clear, and I experienced a profound moment of enlightenment. Your exceptional teaching skills and ability to break down complex ideas into understandable components have truly been an eye-opener for me. I am deeply grateful for your efforts in creating such an informative and insightful resource.

[@PegaAnalytics]

Thank you so much!

[@sobha404]

Thanks a bunch for this simplified and clear explanation, it would be a pleasure if you could share with us how could we make dendrograms from Pulsed field electrophoresis Gel , thank you :)

[@PegaAnalytics]

Funny you should ask that ... the following paper is next on my reading list:
"Pulsed-field gel electrophoresis (PFGE) analysis of Listeria monocytogenes isolates from different sources and geographical origins and representative of the twelve serovars"
www.academia.edu/111312006/Pulsed_field_gel_electrophoresis_PFGE_analysis_of_Listeria_monocytogenes_isolates_from_different_sources_and_geographical_origins_and_representative_of_the_twelve_serovars

[@PegaAnalytics]

I've looked at this in a bit more detail, and to be honest, handling these type of data is beyond my area of expertise. I did find some general information that I found helpful:
A guide to interpreting electrophoresis gels:
bento.bio/resources/bento-lab-advice/interpreting-electrophoresis-gels-with-bento-lab/#:~:text=The%20smallest%20bands%20are%20at,is%20up%20the%20ladder%20scale.
(pulsed-field addressed larger DNA molecules but I presume the principles on interpretation remain the same).
Any analytical technique requires digital data. I found this:
Data processing of pulsed-field gel electrophoresis images
www.ncbi.nlm.nih.gov/pmc/articles/PMC6940661/
The data processing would seem to me the critical step, which will ultimately result in the generation of tabulated data that would be amenable to cluster analysis. The columns of this tabulation would correspond to metrics that describe the banding, which each sample being represented by a row.
I would guess that this data processing is integrated into most laboratory systems that produce pulsed-field electrophoresis gel?

[@SnowCat1997]

Thank you so much this is really easy to understand

[@PegaAnalytics]

Glad it was helpful!