Bioconductor ChIPseeker

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ChIPseeker

2 days ago Anton01 • 0

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ChIPseeker

4 weeks ago Henry ▴ 10

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ChIPseeker

updated 6 months ago by James W. MacDonald 65k • written 6 months ago by inna.gur • 0

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ChIPseeker

updated 6 months ago by James W. MacDonald 65k • written 6 months ago by Jones • 0

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ChIPseeker

updated 9 months ago by kyliecode • 0 • written 3.8 years ago by mwong043 • 0

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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k

Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.

Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k

Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…

Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0

The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.

Comment: Ensembl plants at annotationHub? by Daniele • 0

Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!

Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k

If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?

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Rsubread counting peaks ATACseq

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