The number of isoforms should be (2^n) - (1) and not 2^n (as mentioned at 26:25). Every exon has 2 possibilities and one is subtracted because there is also a state where no exon is present.
the Prof said that in DESeq, Sj is estimated based on each condition separately, but the paper only shows that the variance is estimated that way, not the size factor. Also, I dont think it is necessary to estimate the sequencing depth factor within conditions only. This would make the calculation of fold change impossible, since the mu for each gene is on a different scale.
38:26 what’s the rationale for chi-squared distribution to answer the original modeling? It sounds like the probability is only dependent on the number of parameters and the quality of modeling. Or, in other words, why can we use it for any H0 and H1?
Anyone know how come when one particular sample had twice as many reads as the other, the scaling factor would be two? Though it would be square root 2 or something
This video is very interesting. Makes it very easy to understand how RNA-Seq platform works
The number of isoforms should be (2^n) - (1) and not 2^n (as mentioned at 26:25). Every exon has 2 possibilities and one is subtracted because there is also a state where no exon is present.
It's not easy to understand this complicated stuff, but your explanation is really helpful for me to be clear about it. Thank you very much!
great explanation of the hypergeometric test. finally got it
wonderful lecture on RNA-seq
the Prof said that in DESeq, Sj is estimated based on each condition separately, but the paper only shows that the variance is estimated that way, not the size factor. Also, I dont think it is necessary to estimate the sequencing depth factor within conditions only. This would make the calculation of fold change impossible, since the mu for each gene is on a different scale.
Object modeling is a fundamental tool for analyzing and expressing data requirements. Which aspects seem easiest and most difficult for you?
56:20 principal component analysis PCA
Great class. Thank you.
If there is n no of exon ,there there could be 2^n -1 isoform?
Suppose for 3 exon a,b,c . The Exons are a,b,c,ab,ac,bc,abc .so total 7 isoform not 8
50:20 hypergeometric test
Interesting talk. I have a query that Is it possible to predict bacterial transcription start sites (TSS) using RNA-Seq ??
38:26 what’s the rationale for chi-squared distribution to answer the original modeling? It sounds like the probability is only dependent on the number of parameters and the quality of modeling. Or, in other words, why can we use it for any H0 and H1?
42:35 if this is normalization we use for gene expression, what’s the purpose of rpkm?
44:18 how is q_ip dependent on p based on the first equation?
Anyone know how come when one particular sample had twice as many reads as the other, the scaling factor would be two? Though it would be square root 2 or something
this is 9 years old, do you have plans to update it?
Currently there are no plans to update this course.
50:00 "The mean value theorem" lol