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limma

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BioMartGOGeneSets allele_freq biomaRt getBM

7 hours ago • updated 2 hours ago Abiologist • 0

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DESeq2 PCAplot RNA-Seq DesignModel

updated 50 minutes ago by Michael Love 42k • written 22 hours ago by shaunpeterson • 0

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STRINGdb

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DESeq2

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ensembl ensembldb plant arabidopsis thaliana annotationhub

updated 16 hours ago by Daniele • 0 • written 5.5 years ago by Guido Hooiveld ★ 4.0k

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masigpro clustering

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8 results • Page 1 of 1

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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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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

Rsubread counting peaks ATACseq

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