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Batch Correction
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3
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1.8k
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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 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.2k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 5.0 years ago by
Kevin Blighe
★ 4.0k • written 5.0 years ago by
lucasmiranda42
• 0
5
votes
3
replies
768
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 5.1 years ago by
James W. MacDonald
67k • written 5.1 years ago by
MT
▴ 10
0
votes
3
replies
1.1k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.3 years ago by
Rory Stark
★ 5.2k • written 5.3 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 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
wunderl
▴ 40
4
votes
4
replies
1.6k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.5 years ago by
Michael Love
43k • written 5.5 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 5.7 years ago by
Vladimir Kiselev
▴ 150 • written 5.7 years ago by
hamza_karakurt
▴ 60
7 results • Page
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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