#34 Lockdown Learning Bioinformatics-along: MA and Volcano plots
- – Nice videos. lt br gt But I think the p value threshold should be adjusted for multiple testing for example usiung Benjamini Hochberg looking for the highest p value for which p i lt phi i m is true with i being the rank of the p value m the number of tests and phi the significance 0.05 . lt br gt lt br gt You could also adress how to do this filtering using SAM statistics Wentian Li et al 2012 Journal of Bioinformatics and Computational Biology amp Tusher et al 2001 PNAS . How to plot a curve function etc.
- – Hi I was wondering if you knew how to find out specifically how many genes were upregulated on your volcano plot I know it is the ones on the right but would like to know how to get the exact number thanks Great video too Amy
- – Helpful video What graphics drawing device are you using to write draw on MS Whiteboard
Countdown 0 00 Introduction 5 01 MA Plot 10 02 Jacob s Picture of the Day 25 47 Volcano Plot 27 04 Interactive Volcano Plot 52 23 In lesson 34 we look at some of the more common visualisations for differential expression analysis the MA plot and the volcano plot. Walk through a practical introduction to bioinformatics skills with me while working from home during the Covid 19 pandemic. Aimed at wet lab types who want to take this unique and strange opportunity to begin learning some bioinformatics. I am going to begin at the beginning and take it nice and slow. Our first aim will be to develop the skills required to analyse and visualise a covid relevant RNA Seq dataset.