Bioconductor Gene set enrichment analysis

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typo NES rwikipathways downregulated genes gene set enrichment analysis

updated 5.9 years ago by alex.pico ▴ 30 • written 6.3 years ago by Fischer-philipp ▴ 30

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1.2k

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STRINGdb stringdb gene set enrichment analysis software error go

6.3 years ago wsciekly.maciek ▴ 10

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2.1k

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rsbml piano libsbml gene set enrichment analysis

updated 6.3 years ago by Michael Lawrence ★ 11k • written 6.3 years ago by jan.strauss • 0

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2.4k

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limma gene set enrichment analysis

updated 6.4 years ago by Aaron Lun ★ 28k • written 6.4 years ago by khandarius ▴ 20

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5.2k

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clusterprofiler gene set enrichment analysis enricher sc-rnaseq

updated 6.6 years ago by Guangchuang Yu ★ 1.2k • written 6.6 years ago by atakanekiz ▴ 30

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1.7k

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clusterProfiler gseGO gene ontology go semantic similarity gene set enrichment analysis

6.7 years ago jan.soderman • 0

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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

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Comment: Use of limma R package with targeted proteomics for DE analysis

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

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