Bioconductor PickSoftThreshold

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wgcna picksoftthreshold scale-free topology co-expression network

6.7 years ago marcantoine.guery • 0

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wgcna picksoftthreshold

6.8 years ago aditi ▴ 20

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wgcna sft picksoftthreshold threshold rnaseq

updated 6.9 years ago by Peter Langfelder ★ 3.0k • written 6.9 years ago by Fabricio Almeida-Silva ▴ 40

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rnaseq wgcna picksoftthreshold

updated 8.2 years ago by Lluís Revilla Sancho ▴ 760 • written 8.2 years ago by divara01 • 0

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WGCNA pickSoftThreshold power RNA-Seq

updated 8.9 years ago by Peter Langfelder ★ 3.0k • written 8.9 years ago by mrodrigues.fernanda ▴ 10

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.

Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k

You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…

Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k

The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…

Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0

Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

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