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Showing :
removebatcheffect
•
reset
2
votes
2
replies
284
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
5 weeks ago
sukeshinik5
▴ 20
17
votes
9
replies
6.9k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 6 weeks ago by
James W. MacDonald
67k • written 8.4 years ago by
ompandey
▴ 10
4
votes
4
replies
1.1k
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
4 months ago
sukeshinik5
▴ 20
0
votes
2
replies
1.2k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
22 months ago
dqt
• 0
0
votes
5
replies
4.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.8 years ago by
ATpoint
★ 4.5k • written 3.6 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
935
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 4.7 years ago by
Gordon Smyth
51k • written 4.7 years ago by
Sam
▴ 10
5
votes
7
replies
3.0k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.4 years ago
altintas.ali
• 0
1
vote
6
replies
1.9k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.5 years ago by
James W. MacDonald
67k • written 5.5 years ago by
Biologist
▴ 120
2
votes
5
replies
4.5k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
6.3 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.7k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 6.9 years ago by
Vladimir Kiselev
▴ 150 • written 6.9 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
11k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 7.2 years ago by
Gordon Smyth
51k • written 7.2 years ago by
lirongrossmann
▴ 80
9
votes
8
replies
9.6k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 7.2 years ago by
Gordon Smyth
51k • written 10.3 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.6k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
7.5 years ago
aina.jene
▴ 10
2
votes
2
replies
2.3k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 7.5 years ago by
sina.nassiri
▴ 130 • written 7.5 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.5k
views
Re-use limma beta coefficients
limma
removebatcheffect
7.9 years ago
Keifa
▴ 10
3
votes
6
replies
2.7k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.0 years ago by
Jakub
▴ 50 • written 8.0 years ago by
amoltej
▴ 10
0
votes
3
replies
1.6k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Jenny Drnevich
★ 2.0k
4
votes
5
replies
2.9k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
g.atla
▴ 10
9
votes
10
replies
13k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 8.8 years ago by
Bernd Klaus
▴ 610 • written 8.8 years ago by
Ekarl2
▴ 80
19 results • Page
1 of 1
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Comment: Question about using LRT test for time course experiments with DESeq2
by
James W. MacDonald
67k
You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…
Comment: Question about using LRT test for time course experiments with DESeq2
by
Denise
• 0
Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…
Answer: featureCounts segmentation fault with large chromosomes
by
vkkodali
▴ 10
Thanks to @yangliao this issue is fixed in subread v2.0.8
Comment: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
by
ATpoint
★ 4.5k
For the general audience, reticulate / python (which basilisk depends on / wraps) requires explicit declaration of integers, so one needs i…
Answer: Average expression of genes across replicates
by
ATpoint
★ 4.5k
Not sure what you're asking. The average expression across all samples is what the `baseMean` column of `results()` returns. This is simply…
Votes
Answer: featureCounts segmentation fault with large chromosomes
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
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