User: nickbern92

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nickbern920
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Posts by nickbern92

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Answer: A: Normalization of RNA-seq data: between samples and within samples
... Interesting. I guess I'm still wondering if it's necessary to do between samples normalization after within samples normalization regardless in any situation.   So TMM and DESeq both expect raw counts, but their assumptions for their formula's to a rookie like me don't seem violated by TPM.    ...
written 3.5 years ago by nickbern920
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Normalization of RNA-seq data: between samples and within samples
... I've been looking into normalization more and more, and I was wondering about a few things that perhaps some of you might know the answer to or want to discuss So their exists within samples normalization (TPM or others), i.e. relative abundances and between samples normalization (TMM or others), b ...
rnaseq normalization tmm tpm written 3.5 years ago by nickbern920
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Comment: C: Variance filtering prior to RNA-seq differential expression
... Oh cool. Thanks for the info! ...
written 3.6 years ago by nickbern920
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Comment: C: clustering RNA-Seq data and performing gene set enrichment analysis
... Did you ever get an answer? ...
written 3.6 years ago by nickbern920
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Comment: C: Variance filtering prior to RNA-seq differential expression
... I' new to rna seq analysis. So pardon my ignorance. Why is variance filtering hardly ever a good idea, and almost certainly not with RNA-seq data? What if your downstream analysis is a clustering algorithm instead of differential expression?   Best ...
written 3.6 years ago by nickbern920

Latest awards to nickbern92

Great Question 3.5 years ago, created a question with more than 5,000 views. For Normalization of RNA-seq data: between samples and within samples
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Normalization of RNA-seq data: between samples and within samples

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