Thank you, this explains why using the p.adjust(method="fdr") function in R yields "repeated" p-values. I thought that was an error of some sort but turns out that's just how this algorithm works. Great video
Thank you for the detailed explanation! 1:12 May I know if both adjusting the significance level and adjusting p value result in the same conclusion, how do we decide which one to use? I see most of the papers use adjusted p value...
You will come to the same conclusion. In a paper, it might be confusing if you use different significance levels in different test. It is therefore easier if you use just one alpha (usually 0.05) and adjust the p-values.
@@tilestats Understood :) Thank you so much for your prompt reply. May I ask 2 questions? 1) Is the term "FDR adjusted p-value" interchangeable with "q-value"? 2) For RNA sequencing, I have significant DEGs when using p
FDR adjusted p-values usually refer to BH adjusted p-values or q-values. To see the difference, watch this video: ruclips.net/video/T6J4b-WWebM/видео.html You can still use, for example, GSEA with a ranked gene list based on log2FC as I show in this video: ruclips.net/video/EF94wPaqXM0/видео.html
Thanks for the video!- what about if 2 original p-values are identical? does the rank follow an incremental order or are they ranked the same value? for example: 0.002, 0.003, 0.003 and 0.004. Is 0.003 ranked as 2 and 3; both 2; or both 3? And is the total of ranks 3 or 4? - Thanks!
Thanks for the video! I think I roughly understand the concept for the FDR, but have some trouble interpreting the output p.adjust gives me in R for "Benjamini-Hochberg". From this video I would conclude: I compare each adjusted p-value against the a priori chosen FDR (eg. 0.05 or 0.1) to determine, whether H_0 should be rejected. Am I correct?
At 10:11, could you elaborate what you mean by "The ORIGINAL BH method assumes that the null hypothesis is true for all test", in the context of this video?
To compute BH adjusted p-values in the function "p.adjust" you set the argument "method" to either BH or fdr. Benjamini & Hochberg (1995) ("BH" or its alias "fdr")....
Thank you, this explains why using the p.adjust(method="fdr") function in R yields "repeated" p-values. I thought that was an error of some sort but turns out that's just how this algorithm works. Great video
I study advanced stats for a master's and this is just straight amazing. thank you!
Thank you!
Clear and perfect explanations! You are wonderful!
Awesome explanation! Thank you very much
Very clear, concise, & thorough explanations. Thank you!
Thank you!
Excellent explanation - my compliments!
Great video, life saver for my exam :)
this is the clearest explanation i've ever seen! thanks for sharing!!!
Thank you!
Thank you for the detailed explanation! 1:12 May I know if both adjusting the significance level and adjusting p value result in the same conclusion, how do we decide which one to use? I see most of the papers use adjusted p value...
You will come to the same conclusion. In a paper, it might be confusing if you use different significance levels in different test. It is therefore easier if you use just one alpha (usually 0.05) and adjust the p-values.
@@tilestats Understood :) Thank you so much for your prompt reply. May I ask 2 questions?
1) Is the term "FDR adjusted p-value" interchangeable with "q-value"?
2) For RNA sequencing, I have significant DEGs when using p
FDR adjusted p-values usually refer to BH adjusted p-values or q-values. To see the difference, watch this video:
ruclips.net/video/T6J4b-WWebM/видео.html
You can still use, for example, GSEA with a ranked gene list based on log2FC as I show in this video:
ruclips.net/video/EF94wPaqXM0/видео.html
excellent explanation！Thanks！
Thank you!
excellent explanation
Thank you!
Huge help！Thanks❤️❤️
Thank you!
Thanks for the video!- what about if 2 original p-values are identical? does the rank follow an incremental order or are they ranked the same value? for example: 0.002, 0.003, 0.003 and 0.004. Is 0.003 ranked as 2 and 3; both 2; or both 3? And is the total of ranks 3 or 4? - Thanks!
Both as 3. For ties in p-values, you take the largest joint rank. So the ranks in this example will be: 1 3 3 4.
Awesome - thanks!
Thanks for the video!
I think I roughly understand the concept for the FDR, but have some trouble interpreting the output p.adjust gives me in R for "Benjamini-Hochberg".
From this video I would conclude: I compare each adjusted p-value against the a priori chosen FDR (eg. 0.05 or 0.1) to determine, whether H_0 should be rejected. Am I correct?
Yes, you are correct!
At 10:11, could you elaborate what you mean by "The ORIGINAL BH method assumes that the null hypothesis is true for all test", in the context of this video?
I think this video explains it
ruclips.net/video/T6J4b-WWebM/видео.html
is BH adjusted p-value method same as "FDR" method in R?
To compute BH adjusted p-values in the function "p.adjust" you set the argument "method" to either BH or fdr.
Benjamini & Hochberg (1995) ("BH" or its alias "fdr")....
@@tilestats thanks