User: telroyjatter

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telroyjatter150
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Posts by telroyjatter

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Comment: C: Methods to interrogate RNA-seq
... Yes this is helpful. Thanks, Kevin! ...
written 28 days ago by telroyjatter150
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Comment: C: Methods to interrogate RNA-seq
... It is enough to get started. I don't even have data. I just want to create a list of all of the methods, with their respective applications, that can be used to mine, interrogate, and extract knowledge from an RNA-seq dataset (or *omics datasets more generally). ...
written 4 weeks ago by telroyjatter150
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Comment: C: Methods to interrogate RNA-seq
... Or in the entire dataset, for example some methods include an entire counts matrix rather than just a list of DEGs or the counts of only DEGs. ...
written 4 weeks ago by telroyjatter150
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Comment: C: Methods to interrogate RNA-seq
... Let's say the tissue is from brain, and we want to understand how the administration of a drug affects gene expression. ...
written 4 weeks ago by telroyjatter150
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Methods to interrogate RNA-seq
... Let's say you have an RNA-seq counts matrix for two experimental groups, and you have already generated your table of differentially expressed genes. Generally speaking, what are the best ways to interrogate this dataset? The ones I can think of: - Gene ontology enrichment - WGCNA and/or MEGEN ...
rna-seq written 4 weeks ago by telroyjatter150 • updated 29 days ago by Kevin Blighe66k
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Comment: C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
... This is my experience the vast majority of the time. And I think the saddest part of it is that the bioinformaticians who analyze these underpowered studies and sign off on using raw p-values (example I gave in a reply to the top answer: https://www.nature.com/articles/nm.4386 ; "An individual gene ...
written 9 weeks ago by telroyjatter150
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Comment: C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
... > Absolutely depends on the system and the size of the effects. I'd guess for studies in model organism or cell lines, probably yes. Follow-up: If 4-8 samples is probably sufficient for cell lines and model organisms, but most of those tools take as input DE genes which aren't sufficiently power ...
written 9 weeks ago by telroyjatter150
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Comment: C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
... I appreciate your points. Are there established methods for doing power analyses to detect pathways, correlation structures, genotype-expression relationships etc.? The issues I see with what I like to call "behavioral neurogenetics" are part of the general workflow I see in a lot of papers: 1. Ru ...
written 9 weeks ago by telroyjatter150
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Comment: C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
... There are studies in top journals that use human tissue for RNA-seq, but the sample sizes are too small to where the adjusted p-values don't show any DEGs. Here is one example: https://www.nature.com/articles/nm.4386 "An individual gene was called differentially expressed if the P-value of its t-st ...
written 9 weeks ago by telroyjatter150
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Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
... From the power analysis tools I've seen for RNA-seq, I feel like many published RNA-seq studies are wildly underpowered but no one ever seems to bat an eye about it. I very often see RNA-seq studies with 6, 8, or 10 samples per group, and from the power analysis tools I've looked at (https://cqs-vum ...
power forum sample size rna-seq statistical power written 10 weeks ago by telroyjatter150 • updated 9 weeks ago by pm201290

Latest awards to telroyjatter

Prophet 9 weeks ago, created a post with more than 20 followers. For Am I crazy, or are most published RNA-seq studies vastly underpowered?
Appreciated 9 weeks ago, created a post with more than 5 votes. For Am I crazy, or are most published RNA-seq studies vastly underpowered?

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