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Batch Correction
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3
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3
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1.9k
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fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq
integration
batch correction
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.3k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 5.1 years ago by
Kevin Blighe
★ 4.0k • written 5.1 years ago by
lucasmiranda42
• 0
5
votes
3
replies
782
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 5.2 years ago by
James W. MacDonald
67k • written 5.2 years ago by
MT
▴ 10
0
votes
3
replies
1.2k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.4 years ago by
Rory Stark
★ 5.2k • written 5.4 years ago by
rm1238
• 0
1
vote
1
reply
1.1k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
wunderl
▴ 40
4
votes
4
replies
1.7k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
wunderl
▴ 40
4
votes
5
replies
2.1k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.8 years ago by
Vladimir Kiselev
▴ 150 • written 5.8 years ago by
hamza_karakurt
▴ 60
7 results • Page
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Comment: Newbie Question - adding metadata to an analysis
by
James W. MacDonald
67k
You don't need to generate an `ExpressionSet`, as you already have a `GeneFeatureSet`, which extends `eSet` and is a better fit for what yo…
Comment: Newbie Question - adding metadata to an analysis
by
Bryan H
• 0
Thanks for the documentation. I have most of it working, except for the most critical step - incorporating the new metadata with the datase…
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
Thank you for confirming that the foldchange is log2
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
This solved it!
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
Perfect! Thank you so much!
Votes
Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Answer: Package `not available for Bioconductor version '3.20'` when it should be
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
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