Bioconductor Ruvseq

Showing : ruvseq • reset

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10k

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deseq2 r ruvseq normalization rnaseq

10.5 years ago nickp60 • 0

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3.2k

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edgeR ruvseq rnaseq isoforms

10.7 years ago sergio.espeso-gil • 0

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6.1k

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deseq2 ruvseq sizefacotrs

updated 10.7 years ago by davide risso ▴ 980 • written 10.7 years ago by Assa Yeroslaviz ★ 1.5k

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3.2k

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ruvseq ruv

updated 10.7 years ago by davide risso ▴ 980 • written 10.7 years ago by Pauly Lin ▴ 160

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4.5k

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RUVseq logFC edgeR

10.7 years ago Marie • 0

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3.9k

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RUV ruvseq rnaseq

10.7 years ago sergio.espeso-gil • 0

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1.6k

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RUVSeq

11.4 years ago • updated 11.3 years ago davide risso ▴ 980

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3.5k

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ruvseq RUVs EDA

11.4 years ago • updated 11.3 years ago asif.zubair • 0

108 results • Page 3 of 3

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Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0

You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…

Answer: Array weights in dpcDE by Gordon Smyth 53k

The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…

Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k

Try the vignette which has a lot of information on these type of questions.

Comment: limpa analysis advice by Gordon Smyth 53k

The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …

Comment: limpa analysis advice by SamGG ▴ 360

Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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