See all my videos at www.tilestats.com/ 1. How to adjust the significance level (00:47) 2. How to adjust the p-values (03:28) 3. Graphical illustration (05:56) 4. BH vs Bonferroni (08:30)
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
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?
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: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-T6J4b-WWebM.html You can still use, for example, GSEA with a ranked gene list based on log2FC as I show in this video: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-EF94wPaqXM0.html
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?
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!
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")....
