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 :)
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?
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
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.
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!
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.
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?
The ranking in example is too perfect regarding lowest log2fc being lowest p val as well. What if log2fc is lowest but pval isn’t lowest? Or should we trust calculated ranking metrics as final ranking?
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!
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?
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/
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Thanks Brandon! First of all, it helped me to understand how to make a ranking file for GSEA then the concepts behind the algorithm.
Such a simplified and intuitive explanation of GSEA. Loved it! Thank you so much for putting this out!
😁😁😁
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 :)
Respect! Thank you for explaining soooo easy to understand! Hope to give you many thumbs👍
thank you so much for this video, and thank you SO SO SO much for sharing the slides out
You are genius, it is an amazing video, Many thanks !, please make more videos about GSEA ! :)
It is a really great explanation video for GSEA. Many thanks!
Amazing. Thank you for explaining it so well!
Thank you very much for your clear explanation! Awesome!
Thank you for doing this! great explanation, can you also do a video for GSVA (gene set variation analysis) ?
Wow, amazing explanation. I got more insights. Thanks!
Great explanation! Thank you!
Just what I needed. Thanks
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?
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
Nice explanation!
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.
I need some helps to understand the relationship between step 1 and step 2: how the graphs or scores in step 1 are used in step 2?
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!
Wow! You are incredibly good. Thank you.
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.
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?
The ranking in example is too perfect regarding lowest log2fc being lowest p val as well. What if log2fc is lowest but pval isn’t lowest? Or should we trust calculated ranking metrics as final ranking?
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!
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?
I couldn't find the excel file, would you please guide me?
Can you also provide the permutation figures? Thank you so much!
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/
Thank you x10000000