Bioconductor RNA Seq

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977

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RNA seq wgcna

updated 5.0 years ago by Peter Langfelder ★ 3.0k • written 5.0 years ago by agustin.gonvi ▴ 20

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892

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sgseq alternative splicing rna seq

updated 4.5 years ago by Leonard Goldstein ▴ 200 • written 4.5 years ago by 116100016 • 0

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3.3k

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batch effect limma rna seq DE

updated 4.1 years ago by Steve Lianoglou ★ 13k • written 4.1 years ago by svlachavas ▴ 830

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1.9k

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rna seq trimmomatic trimming adapter trimming paired analysis

5.0 years ago Mozart ▴ 30

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904

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edger RNA Seq

updated 4.5 years ago by James W. MacDonald 65k • written 4.5 years ago by abf ▴ 30

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1.3k

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limma voom RNA Seq Time-course experiments

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by mahes.muniandy • 0

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654

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RNA seq cpm

updated 4.1 years ago by Kevin Blighe ★ 3.9k • written 4.1 years ago by isabel.pieterse • 0

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783

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rna seq SGSeq Alternative splicing

updated 4.6 years ago by Leonard Goldstein ▴ 200 • written 4.6 years ago by 116100016 • 0

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953

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volcano plot rna seq

updated 4.7 years ago by Michael Love 42k • written 4.7 years ago by adeler001 • 0

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552

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deseq2 likelihood ratio rna seq wald test

updated 4.7 years ago by Michael Love 42k • written 4.7 years ago by adeler001 • 0

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1.6k

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heatmap.2 hierarchical clustering microarray RNA seq DEG

6.2 years ago lawarde.ankita1 ▴ 30

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2.6k

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deseq2 mahattan plot RNA Seq

updated 3.6 years ago by bernatgel ▴ 150 • written 4.6 years ago by adeler001 • 0

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497

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rna seq

4.5 years ago adeler001 • 0

13 results • Page 1 of 1

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Comment: Can I trust the differential expression analysis when the two groups overlap on by BioinfGuru ▴ 30

No worries, wish I could be more help. Plotly provide a [3-D plot][1] function that's pretty simple (the two you did are still 2-D plots, t…

Comment: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k

If you manually compute PCA on VST data, what are the top 5 genes contributing to PC1? https://github.com/thelovelab/DESeq2/blob/devel/R/p…

Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0

I created a DESeqDataSet object using DESeqDataSetFromMatrix function. I don't anticipate any mismatching or mixup of sampleIDs.

Answer: Assymetric MA plot with no overall trend by Michael Love 42k

> so many upregulated genes vs. downregulated, which I think is worrying Take a look at the plotCounts for a couple of the up-regulated …

Comment: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k

I'm wondering about sample table mixup. How have you merged your sequencing data with the phenotype data (`colData`)?

Votes

Answer: Can log2cpm be used for proteomics data normalization?

Ensembl 112 has been released.

A: Diffbind results - non uniform width

A: Different logFC (log2foldchange) values for genes from limma-voom and other too

Answer: Error EPICv2 ChAMP

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