Some of the best teaching content on KZbin! Thank you so much and well done! 😊
@AvniMann-p4m2 ай бұрын
i just love your videos please upload videos on population structure analysis and creating plot of population structure using fast-structure only with huge SNP dataset of about 10 lakh SNPs
@amirtemer7215 ай бұрын
I have to put your channel in my CV 😂. Thank you so much ^^
@mayconmarcao45545 ай бұрын
Very interesting and important topic. deseq2 is really powerful but requires different levels of understanding to be used properly. What do you mean by “doesn’t affect the fit” ? In case of a DE analysis can the DEGs be different depending the order we specify the factors in the design matrix? - not even talking about interaction terms Thanks !
@SinergiasHolisticas5 ай бұрын
Love it!!!!!!!!!
@lexieoppong29465 ай бұрын
Thank you for this video! Very helpful! I have a question, if you do not mind. What would the design look like if you are controlling for multiple treatments? Would it be something like this: design = ~treatment1+treatment2+treatment3+genotype
@lanternofthegreen5 ай бұрын
Yes, but put "genotype" at the beginning. And also if you are interested in interaction terms, it would be: design = ~ genotype + treatment1 + treatment2 + treatment3 + genotype:treatment1 + genotype:treatment2 + genotype:treatment3 If you are applying each treatment separately though, meaning that your design matrix looks something like this: genotype treatment sample1 I NONE sample2 II treatment1 sample3 I treatment2 sample4 II treatment3 then you just do genotype+treatment+genotype:treatment as shown in the video.
@qwerty111111225 ай бұрын
0:10 what is this molecule? CH3OF?
@a.k.nikson39875 ай бұрын
Great !
@HominidPetro5 ай бұрын
In case 1, you said DESeq2 fits the count data to a linear model. Did you mean a negative binomial model?
@suspect_device885 ай бұрын
The model that is fit to the counts data is a negative binomial generalised linear model which is still a linear model.
@lanternofthegreen5 ай бұрын
I always do "a + b + a:b" and pick the results I want from it. Trying to work with a+b or a:b alone confuses me.
@qwerty111111225 ай бұрын
As you should usually, unless a:b is very small and not significant, then just use a+b. Simpler equations are subjectively better. You can use "a*b" as shorthand for "a + b + a:b". It makes it a lot shorter when you have an experiment like "a*b*c", short for "a+b+c+a:b+a:c+b:c+a:b:c"
@lanternofthegreen5 ай бұрын
@@qwerty11111122 Damn I didn't know that. Thanks a lot!
@arezoorahimi47925 ай бұрын
Hi Thanks for your great channel! I am working on identifying B cell clusters in peritoneum. Could you please provide me gene markers to identify these subpoulations? Thanks