Bioconductor Diffcoexp

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diffcoexp

written 2.5 years ago by martin.grigorov ▴ 10

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diffcoexp

5.4 years ago Priyanka Jain ▴ 20

2 results • Page 1 of 1

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Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k

As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…

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, …

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