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removeBatchEffect
•
reset
2
votes
2
replies
527
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
7 months ago
sukeshinik5
▴ 20
17
votes
9
replies
7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7 months ago by
James W. MacDonald
68k • written 8.9 years ago by
ompandey
▴ 10
4
votes
4
replies
1.4k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
10 months ago
sukeshinik5
▴ 20
0
votes
2
replies
1.4k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
2.3 years ago
dqt
• 0
0
votes
5
replies
5.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 3.3 years ago by
ATpoint
★ 4.8k • written 4.1 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
1.1k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 5.2 years ago by
Gordon Smyth
52k • written 5.2 years ago by
Sam
▴ 10
5
votes
7
replies
3.3k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.9 years ago
altintas.ali
• 0
1
vote
6
replies
2.1k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
Biologist
▴ 120
2
votes
5
replies
5.0k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
6.7 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.9k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 7.4 years ago by
Vladimir Kiselev
▴ 150 • written 7.4 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
lirongrossmann
▴ 80
9
votes
8
replies
11k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 7.6 years ago by
Gordon Smyth
52k • written 10.7 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.8k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
7.9 years ago
aina.jene
▴ 10
2
votes
2
replies
2.4k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 8.0 years ago by
sina.nassiri
▴ 130 • written 8.0 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.6k
views
Re-use limma beta coefficients
limma
removebatcheffect
8.4 years ago
Keifa
▴ 10
3
votes
6
replies
3.1k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.5 years ago by
Jakub
▴ 50 • written 8.5 years ago by
amoltej
▴ 10
0
votes
3
replies
1.7k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Jenny Drnevich
★ 2.0k
4
votes
5
replies
3.1k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 9.2 years ago by
Aaron Lun
★ 28k • written 9.2 years ago by
g.atla
▴ 10
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 9.3 years ago by
Bernd Klaus
▴ 610 • written 9.3 years ago by
Ekarl2
▴ 80
19 results • Page
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Answer: ROAST for small sets
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52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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