Bioconductor Confounding

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edger confounding

updated 5.4 years ago by Aaron Lun ★ 28k • written 5.4 years ago by Victoria • 0

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limma batch effect design matrix microarray confounding

7.5 years ago svlachavas ▴ 830

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limma voom continuous interactions confounding

8.1 years ago lanhuong ▴ 20

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limma gene expression confounding adjustment paired

9.0 years ago Loodramon • 0

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limma GSA confounding within-pair analysis 450k

9.5 years ago Aileen Bahl ▴ 10

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Comment: DESeq Input from Salmon + tximport/tximeta by ATpoint ★ 4.5k

> If I use gene_counts_length_scaled.tsv as a metric that has already normalized for library size and the average transcript length No, o…

Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Gordon Smyth 51k

`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample. For values much larger than the background, the e…

Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0

Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…

Answer: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k

Given nf-core's pipeline here, you can use rounded counts from `gene_counts_length_scaled.tsv`.

Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k

You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…

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Answer: DESeq Input from Salmon + tximport/tximeta

Answer: featureCounts segmentation fault with large chromosomes

Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion

Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu

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Popular Question to Assa Yeroslaviz ★ 1.5k