User: assaron

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assaron170
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assaron
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Posts by assaron

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Pathway test for reversal of effect (three-condition comparison)
... I got `ranks = (m2 - m1) / (s1 + s2)` where `m2` and `m1` are means, and `s1` and `s2` are standard deviations for the corresponding samples. This better forces top genes to have small variance between AB and zero samples. Btw, I remembered it was used in a published paper, so it may be useful to c ...
written 4 months ago by assaron170
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Answer: A: Pathway test for reversal of effect (three-condition comparison)
... I don't know how to do it properly, but from a practical perspective you can rank genes for GSEA based on comparison (AB or zero) vs A. A signal to noise metric worked fine for me. There top genes would have similar expression levels in AB and zero, while up-regulated in A. ...
written 4 months ago by assaron170
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Answer: A: Is there a name for these charts?
... It's a variant of a barcode plot, or a strip plot, or a rug plot: https://stats.stackexchange.com/questions/190097/whats-the-name-of-this-barcode-like-graph-used-for-visualizing-spread-in-dat ...
written 8 months ago by assaron170
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Answer: A: Cut-off for genesets in GSEA
... Cut-offs are more of performance parameters. Limiting min and max set sizes you limit the time required for the analysis. For large gene sets estimation of is computationally harder compared to smaller gene sets. ...
written 12 months ago by assaron170
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Answer: A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
... I'd recommend changing infinities to the corresponding maximum positive and negative finite values, may be multiplied by a constant > 1. GSEA here is about weighted ranking: you can assign it whatever you like and it would be fine from the method's standpoint. However, when you remove some genes ...
written 13 months ago by assaron170
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Comment: C: GSEA following DESeq2
... As you use R pipeline, I recommend to use R implementation of pre-ranked GSEA: either through fgsea package or clusterprofiler/DOSE interface. It's the same method but much faster. Answering your question, I normally use stat column of DESeq2 results, but your metric should also work fine. ...
written 16 months ago by assaron170
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Comment: C: How do I obtain germline mutation for TCGA samples?
... Yes. You still need a key for the protected data. ...
written 16 months ago by assaron170
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Answer: A: Input all the ranked genes into pre-ranked GSEA?
... While you indeed can input all your genes into GSEA, personally usually select top 12000 expressed genes. This allows to reduce noise from lowly-expressed and non-expressed genes. ...
written 17 months ago by assaron170
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Answer: A: How do I obtain germline mutation for TCGA samples?
... The only way that worked for me was to go to GDC Legacy Archive and download protected vcfs from there. In the new version I couldn't find germline mutation calls anywhere, even in protected MAFs and VCFs. ...
written 18 months ago by assaron170
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Answer: A: How to view all KEGG reactions?
... You can get up-to-date links between kegg reaction IDs and genes using KEGG REST API. You can first find mapping from reactions to enzymes and then from enzymes to human genes: library(KEGGREST) rxn2enz <- keggLink("enzyme", "reaction") enz2hsa <- keggLink("hsa", "enzyme") Replac ...
written 21 months ago by assaron170

Latest awards to assaron

Scholar 8 months ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler

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