User: nk

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nk0
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Posts by nk

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Comment: C: scater/scran with TPMs from Salmon - counts?
... Thank you for your reply Aaron! So you think it shouldn't make a difference for trendVar whether the input is counts or tpm? I am still a bit confused by the documentation of that function though, since it says "Log-transformed values are used as these tend to be more robust to genes with strong e ...
written 19 months ago by nk0
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scater/scran with TPMs from Salmon - counts?
... I am trying to process a scRNA-seq data set generated with SmartSeq2 using `scater` v1.6.1. I quantified gene expression using Salmon and then loaded it into scater with `readSalmonResults` as described in the vignette. I then summarised the transcript-level expression into genes using `sce_gene = s ...
salmon scran scater written 19 months ago by nk0 • updated 19 months ago by Aaron Lun24k
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Comment: C: topGO - Two-tailed (depletion/enrichment) analysis?
... Why would it make more sense to test separately? Wouldn't two separate one-tailed tests actually overestimate significance, which we would have to correct for again? It definitely feels "statistically cleaner" to me to do a two-tailed test for significance first and then check the direction afterwar ...
written 4.7 years ago by nk0
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topGO - Two-tailed (depletion/enrichment) analysis?
... I would like to do a simple GO enrichment analysis with topGO. In theory I believe this should be possible with a simple "classic fisher" test. However, I am not only interested in GO terms that are significantly enriched in significant genes, but also GO terms that are significantly depleted. Whil ...
go topgo written 4.7 years ago by nk0 • updated 4.7 years ago by Gordon Smyth38k

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For topGO - Two-tailed (depletion/enrichment) analysis?

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