Showing : batch effects • reset
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full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 3.6 years ago by 64k • written 3.6 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 3.8 years ago by 64k • written 3.8 years ago by ▴ 20
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.9 years ago anne.bozack • 0
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.2 years ago chendianyu • 0
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adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 4.4 years ago by 64k • written 4.4 years ago by • 0
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8
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1.2k
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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 5.2 years ago by 64k • written 5.2 years ago by • 0
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
6.3 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 6.3 years ago by 64k • written 6.3 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 6.4 years ago by 41k • written 6.4 years ago by • 0
9 results • Page 1 of 1
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Answer: RNASeq time course analysis, missing time points for control by Gordon Smyth 48k
You could fit a spline trend with design matrix `treatment+spline`. Then it won't matter than the control and treatment times don't match u…
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
Thanks James for your helpful response. This particular experimental set up is very common in iPSC studies, where multiple differentiations…
Comment: DESeq2 test for synergistic vs additive effects by Jay • 0
Why is TrtAB - TrtA - TrtB + Control "not really a thing"? i came to this forum answer when attempting to use EdgeR to answer a similar que…
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Votes
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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