Thank you very much! I am Brazilian and I needed to undestand enrichment analysis to do a seminar presentation in my master's. Now I did it, thanks to you :)
You are awesome. Thanks for the simplified version of the gene walking. :-) Can you show how to run venn diagram and volcano plots for scRNAseq dataset? Cheers!
Thank you for the amazing video, however with the running sum why add 1 and deduct 0.5 is this standard? or you can choose a number of your own to add or deduct?
Hi! Thank you so much for this clear and nicely explained video. Could you please also make a video showing GSEA PreRAnked analysis using the broad institute GSEA tool. starting from making a *.rnk file for the RNAseq experiment?
Many thanks, great video! But for the rank, shouldn't it be the -log10(p_adj) * sign(log2FC)? I guess there is not really a wrong or right but using the sign seems cleaner.
good video, just one question: the formula used for the gene ranking was Log2(FC)*-log10(p-value), where does this formula come from? Does it has a proper name? thank you
hi. I really appreciate the simplified explanation. I also have a habit of simulating data using excel sheets so kudos to that! one question is - what are columns A to G in the enrichment calculation sheet? what does cell 6B and 6E mean?
Could I ask a question? If the log10p-value is -inf (-∞, because p-value is almost equal to 0), how could we calculate the log2FC*log10p-value for ranking? Do we need to substitute the -inf to a very small value such as 0.000000001? Thank you very much!
Thank you for your video. I have questions: what these frequencies (9:53) are about and why the cummulative frequency (the left side) is decreasing in B.
oops, seems like I have forgot to attached them during the edits,. you can find it at figure 4 in the website here: www.pathwaycommons.org/guide/primers/data_analysis/gsea/
