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12 months ago
Maria Doyle
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3.1 years ago
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Matthew Ritchie
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shepherl
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DESeq2 multiple groups comparison issues, incorrect log2FC results in a small proportion of genes
deseq2
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Michael Love
42k • written 3.6 years ago by
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BridgeDbR devel package upgraded to BridgeDb 3
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BioCAsia Virtual Meeting, 15-18 October 2020
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3.7 years ago • updated 3.6 years ago
shepherl
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ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
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shepherl
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shepherl
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shepherl
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shepherl
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kayla.interdonato
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kayla.interdonato
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shepherl
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4.1 years ago
Martin Morgan
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4.1 years ago
Matthew Ritchie
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shepherl
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kayla.interdonato
▴ 160 • written 4.1 years ago by
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3.9k
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Deadline for devel branch 3.11 to pass R CMD build and R CMD check
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4.1 years ago
shepherl
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shepherl
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kayla.interdonato
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50 results • Page
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Replies
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?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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