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batch effects
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0
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replies
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
1
vote
1
reply
1.8k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 6.8 years ago by
James W. MacDonald
66k • written 6.8 years ago by
DataFanatic
▴ 10
2
votes
4
replies
1.7k
views
full confounding between batch and treatment effects
batch effects
limma
batch-correction
RNAseq
RUVseq
updated 4.0 years ago by
James W. MacDonald
66k • written 4.1 years ago by
bhakti.dwivedi
• 0
1
vote
8
replies
1.3k
views
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
James W. MacDonald
66k • written 5.6 years ago by
amy16
• 0
0
votes
2
replies
1.3k
views
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
Michael Love
42k • written 6.8 years ago by
Dipro
• 0
0
votes
0
replies
1.2k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
6.8 years ago
vedran.franke
• 0
0
votes
0
replies
893
views
DEG among experimental and control group in MAST
MAST
DEG
batch effects
4.7 years ago
chendianyu
• 0
0
votes
3
replies
859
views
Problem with including batch effects in linear model in LIMMA- samples are removed
limma
batch effects
linear model
updated 4.3 years ago by
James W. MacDonald
66k • written 4.3 years ago by
sandra.murphy
▴ 20
0
votes
0
replies
698
views
adding batch effects as a covariate in additive model in edgeR
edger
batch effects
updated 4.9 years ago by
James W. MacDonald
66k • written 4.9 years ago by
Victoria
• 0
9 results • Page
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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%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
by
jovel_juan
▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
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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