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Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
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Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Hello, This error seems to have returned (R 4.2.2 BioC 3.16.0)? The same code block worked without error until today. ``` > library(Sign…
Answer: RUVr batch correction doubling number of DEGs
No, this sounds like RUV is helping to reduce variance due to unaccounted for batch effects. So it’s helping.
Comment: Ascona Workshop “Biological systems: from first principles to data-driven model
Dear Liam, it's bi-annual, we just submitted a proposal. If it works out, it'll be in 2024, and as it looks now, in early September. Theme:…
Comment: IHW for multiple regression
Indeed, for the two-sided t-test (and similar), the sign of the test statistic is independent of the p-value under the null hypothesis, and…
Comment: edgeR supports continuous covariates?
Hi Yunshun Chen and Gordon Smyth, does edgeR support mixed model? (https://en.wikipedia.org/wiki/Mixed_model)
A: Can't load package "org.Hs.eg.db"
A: edgeR: exactTest, glmFIt or glmQLFit approach?
Answer: on which data type limma::removeBatchEffect can be applyed?
C: WGCNA: Understanding module-trait correlations
A: WGCNA: Understanding module-trait correlations
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