Bioconductor Fella

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FELLA

22 months ago yuhang • 0

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FELLA

22 months ago yuhang • 0

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FELLA

4.2 years ago sergi.picart ▴ 20

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fella

updated 4.2 years ago by sergi.picart ▴ 20 • written 6.9 years ago by cecilia.chiriac • 0

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fella software error

6.1 years ago sergi.picart ▴ 20

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FELLA software error

6.3 years ago sergi.picart ▴ 20

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software error FELLA

updated 7.0 years ago by sergi.picart ▴ 20 • written 7.0 years ago by jnzd_hemaozhang • 0

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

Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…

Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Federico Marini ▴ 180

Jumping in on this - all this started because we want to "do it right", i.e. avoiding the post-hoc filtering on the logFC (which is still w…

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…

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