Showing : batch effects • reset
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full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
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3
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Problem with including batch effects in linear model in LIMMA- samples are removed
limma batch effects linear model
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 20
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.4 years ago anne.bozack • 0
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.7 years ago chendianyu • 0
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adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
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8
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Code to address batch effect in total number of reads/ sample for DEG using Ballgown
differential expression analysis ballgown r batch effects total number of reads
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
7.8 years ago vedran.franke • 0
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Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 10
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Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
deseq2 random effects batch effects RNA-seq rna-seq
updated 26 days ago by • 0 • written 7.8 years ago by • 0
9 results • Page 1 of 1
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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 …
Comment: Limma suqeezeVar by Mengchun • 0
Hi Gordon, Thank you for your reply. I'm working on a proteomics data imputation project, I would like to describe the intensity distribut…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
thank you for your reply. I'm sorry if the question is off topic. the analysis and relative construction of the heatmap was done using bioc…
Answer: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
![Figure1][1]![Figure2][2] [1]: /media/images/d62918c5-2886-44ae-930d-91d292c3 [2]: /media/images/421df232-8a9c-4016-bc4a-431ca57a
Votes
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?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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