User: penny.lane

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penny.lane10
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Posts by penny.lane

<prev • 6 results • page 1 of 1 • next >
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Comparing gene set enrichment across 3+ conditions?
... I typically use GSEA to look for enriched pathways between the conditions of an experiment. While it's clear how to employ it to compare a pair of conditions, I've yet to find an entirely satisfying way to compare holistically across all N conditions of an experiment and I'm wondering what solutions ...
rna-seq gsea written 21 days ago by penny.lane10 • updated 7 days ago by Elucidata40
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Comment: C: GSEA: Does a gene set really have positive and negative enrichment scores?
... Makes sense. Thanks Shawn! ...
written 16 months ago by penny.lane10
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Comment: C: GSEA: Does a gene set really have positive and negative enrichment scores?
... Thanks for the quick response Shawn! Your explanation makes sense. So, what do people typically do to capture enriched gene sets where the genes in the set tend to change under the same conditions, but actually contain a mix of up- and down-regulated genes? The first thing that comes to mind is to r ...
written 16 months ago by penny.lane10
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GSEA: Can a gene set have positive and negative enrichment scores?
... I had thought I understood the meaning of the positive and negative normalized enrichment scores (NES) produced by GSEA, but it just occurred to me I don't know what to expect from a gene set that is enriched both at high and low ranks. For example, some gene sets (e.g., GO biological processes) con ...
gsea written 16 months ago by penny.lane10
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Comment: C: Options for cell type deconvolution from whole blood?
... Yeah, this is one that caught my attention, but according to their website the LM22 signature was designed & validated on microarray data and they warn against applying it to RNA-Seq data. They say they are in the process of deriving and validating a signature for RNA-Seq data, but no release da ...
written 17 months ago by penny.lane10
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Options for cell type deconvolution from whole blood?
... Hello, My colleagues and I have human, whole blood RNA-Seq data from which we would like to estimate the proportions of various immune cell types within each sample and then see how they are changing between samples. We do not, however, have our own matched single cell RNA-Seq data set to help wit ...
rna-seq written 17 months ago by penny.lane10 • updated 11 months ago by E.Earley20

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Popular Question 16 months ago, created a question with more than 1,000 views. For GSEA: Can a gene set have positive and negative enrichment scores?

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