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Showing :
removebatcheffect
•
reset
2
votes
2
replies
534
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
5.4k
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 6.0 years ago by
James W. MacDonald
68k • written 6.0 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
2.5k
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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Comment: DiffBind; Error: No sites have activity greater than filter value
by
etiennedanis
• 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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