Bioconductor PathwayPCA

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pathwayPCA

updated 18 months ago by Kevin Blighe ★ 3.9k • written 18 months ago by Alena • 0

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pathwayPCA Gsea

updated 18 months ago by gabriel.odom • 0 • written 18 months ago by Mikołaj Mierzejewski • 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: 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?

Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0

The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…

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