User: James Cook

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James Cook0
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Posts by James Cook

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Comment: C: Expression thresholds for enrichment analysis of RNA-Seq data
... Thanks for this - I think that makes sense. My problem with low-expressed genes is not so much that I don't think the changes are "real" as such, just that I question how useful they are as indicators of what type of signalling pathways or functional changes are occurring. This might be specific ...
written 5 weeks ago by James Cook0
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Comment: C: Expression thresholds for enrichment analysis of RNA-Seq data
... Yep, my data are already processed with DESeq2 so I'm not too concerned about the inflated fold-change issue, although I still think that, despite the shrinkage there will still be much more of a noise influence on these genes. My main issue is the idea of selecting by expression level rather than ...
written 5 weeks ago by James Cook0
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Expression thresholds for enrichment analysis of RNA-Seq data
... Hi Guys I have a question about filtering genes detected in an RNA-Seq experiment for subsequent enrichment analysis. I know it's common to use a p-value threshold in combination with a fold-change cutoff to define your gene set. However, with my data I tend to find that I have a lot of genes whic ...
rna-seq written 5 weeks ago by James Cook0
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Pre-ranked GSEA on gene clusters
... I'm analysing an RNA-Seq dataset and want to do preranked GSEA to find out what pathways are changing in my dataset. I've read that this type of analysis should be done using ALL the genes detected in the experiment, not just DE genes. This makes sense to me for relatively simple experiments (ie c ...
rna-seq gsea written 11 weeks ago by James Cook0

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