Bioconductor Glmfit

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edger edger main and interaction effects glmfit

updated 7.6 years ago by Aaron Lun ★ 29k • written 7.6 years ago by D ▴ 10

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edger rnaseq glm glmfit

updated 9.5 years ago by Aaron Lun ★ 29k • written 9.5 years ago by alessia.donato • 0

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edger standard error glmfit

9.6 years ago david.hughes • 0

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edger glmfit glmlrt()

updated 10.2 years ago by Aaron Lun ★ 29k • written 10.2 years ago by cadeans • 0

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Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k

it looks above like you have a gene with two non-zero count samples. Also, yes you can use a stricter filter. You cannot estimate the LFC …

Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Ahmed Salah • 0

Thank you very much for your answer. Actually, this is after pre-filtering ```r keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep, …

Answer: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k

> When I specify lfcThreshold instead of post-hoc LFC filtering, some genes with very low expression and biologically negligible change are…

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.

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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