Bioconductor SmallRNA

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deseq2 normalization smallrna ribosomal rna

7.6 years ago mosharrofgeb ▴ 10

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Sequencing miRNA SmallRNA DESeq Sequencing miRNA SmallRNA DESeq

updated 13.4 years ago by Wolfgang Huber ★ 13k • written 13.4 years ago by Wu, Xiwei ▴ 350

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Sequencing SmallRNA edgeR Sequencing SmallRNA edgeR

updated 11.7 years ago by Mark Robinson ▴ 880 • written 11.7 years ago by Danie ▴ 40

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1.9k

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TMM deseq2 smallrna rnaseq

updated 5.5 years ago by António Miguel de Jesus Domingues ▴ 510 • written 5.5 years ago by Konstantinos Yeles ▴ 80

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Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR

updated 11.7 years ago by Steve Lianoglou ★ 13k • written 11.7 years ago by Weng Khong LIM ▴ 10

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Sequencing SmallRNA Microarray limma Sequencing SmallRNA Microarray limma

updated 9.8 years ago by James W. MacDonald 65k • written 9.8 years ago by Jakub Stanislaw Nowak ▴ 70

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matrix DESeq2 SmallRNA dimensions small

2.7 years ago andreia ▴ 10

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1.2k

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mirna riboseq smallrna differential gene expression Job

6.2 years ago Andy Lynch ▴ 120

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1.2k

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smallrna counts

7.6 years ago ribioinfo ▴ 100

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cancer sequencing rnaseq methylation smallrna Job

5.9 years ago Andy Lynch ▴ 120

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940

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counts SmallRNA Normalization

updated 2.4 years ago by hauken_heyken ▴ 80 • written 2.5 years ago by k___ ▴ 30

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DESeq2 SmallRNA

updated 11 weeks ago by Michael Love 42k • written 12 weeks ago by r.r.bioinf • 0

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699

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SmallRNA DESeq2

21 months ago jucosie • 0

13 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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