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batch correction
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3
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3
replies
2.0k
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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 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.5k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
lucasmiranda42
• 0
5
votes
3
replies
869
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
MT
▴ 10
0
votes
3
replies
1.3k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.8 years ago by
Rory Stark
★ 5.2k • written 5.8 years ago by
rm1238
• 0
1
vote
1
reply
1.2k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
wunderl
▴ 40
4
votes
4
replies
1.9k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
wunderl
▴ 40
4
votes
5
replies
2.4k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 6.1 years ago by
Vladimir Kiselev
▴ 150 • written 6.1 years ago by
hamza_karakurt
▴ 60
7 results • Page
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Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Geoff
• 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
parameters of filterByExpr
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