User: coulsonr

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coulsonr10
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Posts by coulsonr

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Comment: C: Calculate S/N ratios from apeglm for GSEA
... Thanks for your reply Mike - yes, seems it's best to stick with the shrunken LFCs. Cheers, Richard. ...
written 5 months ago by coulsonr10
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Calculate S/N ratios from apeglm for GSEA
... Hi, I've been using the shrunken log fold-changes generated by apeglm as the test statistic for gene set enrichment analyses when running the fgsea package. I have seen a paper that suggests the absolute value of Signal-To-Noise is a better metric than LFC: https://bmcbioinformatics.biomedcentral.c ...
fgsea apeglm signal-to-noise ratio written 5 months ago by coulsonr10 • updated 5 months ago by Michael Love25k
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Answer: A: Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
... Thanks Mike, this filtering out of genes with low counts solved the issue. Cheers, Richard. ...
written 14 months ago by coulsonr10
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Comment: C: Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
... Many thanks Mike. I tried setting dds$Rate to dds$Rate - dds$Rate[1], and this failed. However with dds$Rate[11] (the first row in the design matrix with GroupDN==0) it works. Though this produced: Warning messages: 1: In sqrt(diag(sigma)) : NaNs produced 2: In sqrt(diag(sigma)) : NaNs produced 3 ...
written 14 months ago by coulsonr10
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Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
... Hi, I'm running lfcShrink to shrink log2 fold-changes (produced by DESeq2) so I can then use them in a gene set enrichment analysis. The design is (39 samples) :- > pheno.df Group Rate Quartile 4988-043 DN 37.89901 Q1 4988-016 DN 38.92224 Q1 4988-073 DN 26 ...
deseq2 lfcshrink apeglm written 14 months ago by coulsonr10

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