Bioconductor HERVs

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tximport HERVs edgeR DESeq2

updated 4.7 years ago by Michael Love 43k • written 4.7 years ago by rodrigo.duarte88 ▴ 40

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deseq2 HERVs low counts prefiltering dispersion estimates

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by rodrigo.duarte88 ▴ 40

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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…

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Comment: limpa analysis advice

Answer: When to use edgeR or limma

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