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batch correction
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3
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1.6k
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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 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
p.joshi
▴ 40
0
votes
1
reply
989
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
lucasmiranda42
• 0
5
votes
3
replies
619
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
MT
▴ 10
0
votes
3
replies
956
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
rm1238
• 0
1
vote
1
reply
1.0k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
wunderl
▴ 40
4
votes
4
replies
1.4k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
wunderl
▴ 40
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.1 years ago by
Vladimir Kiselev
▴ 150 • written 5.1 years ago by
hamza_karakurt
▴ 50
7 results • Page
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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