Showing : batch effects • reset
2
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full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.0 years ago by 66k • written 4.1 years ago by • 0
1
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1
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1.8k
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Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 6.8 years ago by 66k • written 6.8 years ago by ▴ 10
1
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8
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1.3k
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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 5.6 years ago by 66k • written 5.7 years ago by • 0
0
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0
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893
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.7 years ago chendianyu • 0
0
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0
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2.0k
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
4.4 years ago anne.bozack • 0
0
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3
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859
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Problem with including batch effects in linear model in LIMMA- samples are removed
limma batch effects linear model
updated 4.3 years ago by 66k • written 4.3 years ago by ▴ 20
0
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0
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698
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adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 4.9 years ago by 66k • written 4.9 years ago by • 0
0
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0
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1.2k
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
6.8 years ago vedran.franke • 0
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1.3k
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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 6.8 years ago by 42k • written 6.8 years ago by • 0
9 results • Page 1 of 1
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Replies
Answer: Normalisation using clinical traits in RNA seq using DESeq2 by ATpoint ★ 4.2k
See the vignette, it's a FAQ: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-st…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Please could you comment on this @rory
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by Wei Shi ★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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