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edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 3 hours ago by 52k • written 17 hours ago by • 0
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GBCC2025: New Scholarship Opportunities Available!
Community Conference GBCC2025 Bioconductor
7 hours ago Maria Doyle ▴ 100
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27
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Blank gene_id in featureCounts
featureCounts Rsubread
15 hours ago Meg • 0
0
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4
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322
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Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 12 hours ago by 68k • written 16 hours ago by • 0
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FCS 32 support going backwards?
flowCore
22 hours ago Oliver • 0
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
updated 9 hours ago by 68k • written 1 day ago by ▴ 10
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Limma suqeezeVar
limma
2 days ago • updated 13 hours ago Mengchun • 0
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
19 days ago • updated 3 hours ago caroline.zanchi ▴ 10
8 results • Page 1 of 1
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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
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Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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