Can you please give a step by step Process of this gsea analysis.. Like from a gsea file download to create .cls file and run gsea... It will be very helpful for the beginners like me...
@colemanhk
4 жыл бұрын
It seems the speaker used some slides from a guy namely "Gonzalo G ómez, PhD". You can find the corresponding slides by google search of this name. The following link is one of the results. bioinfo.cnio.es/files/training/Functional_Analysis_Course/UBio_FuncAnalysis_GSEA.pdf
@ivanagrbesa8592
4 жыл бұрын
Really well and profoundly explained. Excellent! Very useful
@archis2112
4 жыл бұрын
Could you please share the R code used to convert differentially expressed genes list to rank list. Thanks.
@meenalmane8848
4 жыл бұрын
very nice explanation.thank you very much.
@youvikasingh7955
4 жыл бұрын
Nice explanation.. Could you please share your code for preparing.rnk file. Thanks
@jacklu1611
4 жыл бұрын
really great explaining. Thanks a lot
@user-lc3rq4nw1u
4 жыл бұрын
when calculating the denominator of Hits, whether the FC is abs or not?thx
@vijayfood
4 жыл бұрын
at 17:32 time, there is a mention that sigma is the sum of all fold changes of my DE gene set, since my gene set can have both upregulated and downregulated genes then sigma can be closer to zero or can be even negative. or is Sigma also a modulus of the sum of fold changes ?
@vijayfood
4 жыл бұрын
Also, a doubt with N, is this the total number of genes in the actual array which can be very high (like total genes in the microarry/RNA seq expt) or is this the total number of DE genes after FDR and Fold change cut-off was imposed. is this true if the genes in my list (DE genes list = N) is quite low and I miss a gene the penalty imposed will be high as compared to if N has more genes e.g {-1/(80-70)} vs {-1/(400-70)}
@LnNJBFANZ
4 жыл бұрын
@@vijayfood N is the total number of genes in the gene set L. The gene set L is created by applying the FDR cutoff of your choice and then ranking the genes by log2FC values. Like in the video and also in the research paper describing this method, sigma refers to the sum of the ABSOLUTE VALUES of all the fold change values of genes present in the set S. I suggest you read the paper for further clarification: www.pnas.org/content/102/43/15545
@TK_Big
5 жыл бұрын
I'm confused when I prepared a input data. I have hundreds of DEG which was already selected by filtering with p-value, and whole thousands of raw data (RPKM). Which do I have to use, the selected RPKM from the DEG or the whole RPKM??
@drvishalthapar
4 жыл бұрын
You will select the entire gene list except it needs to be ranked according to your "ranking metric" so if you use p-value then rank the genes in increasing order of p-value and then you have your list of genes for the GSEA in a .RNK file
@sediquabufford2705
3 жыл бұрын
Thank you!
@martinschwill9210
5 жыл бұрын
Are the slide available somewhere? Thank you.
@nathansuek2571
4 жыл бұрын
An excellently explained video! I would also be interested in the slides - since the video isn't high quality enough to read the slides
@sumanmohajan6392
5 жыл бұрын
could you please give such other lecture on bioinformatics in genome study
@drvishalthapar
5 жыл бұрын
Hi Suman, Could you elaborate "Genome Study"? Happy to upload more videos if it's helpful -Vishal
@lifeshortsostandtall
5 жыл бұрын
Great talk
@saintamaria5598
5 жыл бұрын
What do mean. By probe
@saintamaria5598
5 жыл бұрын
@Sadek Abderrahmane thank you :))
@saintamaria5598
5 жыл бұрын
@Sadek Abderrahmane i have a nother question what does it mean if the ES is with minus value ??
@drvishalthapar
5 жыл бұрын
@@saintamaria5598 That means that the genes that are in your gene set are enriched in the down regulated side of your comparison.
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