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Showing :
removeBatchEffect
•
reset
2
votes
2
replies
411
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
4 months ago
sukeshinik5
▴ 20
17
votes
9
replies
7.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 4 months ago by
James W. MacDonald
68k • written 8.7 years ago by
ompandey
▴ 10
4
votes
4
replies
1.3k
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
7 months ago
sukeshinik5
▴ 20
0
votes
2
replies
1.3k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
2.1 years ago
dqt
• 0
0
votes
5
replies
4.9k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 3.1 years ago by
ATpoint
★ 4.6k • written 3.9 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
1.0k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 5.0 years ago by
Gordon Smyth
52k • written 5.0 years ago by
Sam
▴ 10
5
votes
7
replies
3.1k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.7 years ago
altintas.ali
• 0
1
vote
6
replies
2.0k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Biologist
▴ 120
2
votes
5
replies
4.7k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
6.5 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.8k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 7.2 years ago by
Vladimir Kiselev
▴ 150 • written 7.2 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 7.4 years ago by
Gordon Smyth
52k • written 7.4 years ago by
lirongrossmann
▴ 80
9
votes
8
replies
10k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 7.4 years ago by
Gordon Smyth
52k • written 10.5 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.7k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
7.7 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 7.8 years ago by
sina.nassiri
▴ 130 • written 7.8 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.5k
views
Re-use limma beta coefficients
limma
removebatcheffect
8.2 years ago
Keifa
▴ 10
3
votes
6
replies
2.9k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 8.3 years ago by
Jakub
▴ 50 • written 8.3 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 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
Jenny Drnevich
★ 2.0k
4
votes
5
replies
3.0k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 9.0 years ago by
Aaron Lun
★ 28k • written 9.0 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 9.1 years ago by
Bernd Klaus
▴ 610 • written 9.1 years ago by
Ekarl2
▴ 80
19 results • Page
1 of 1
Recent ...
Replies
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell
by
James W. MacDonald
68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20
by
James W. MacDonald
68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2
by
caroline.zanchi
• 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org
by
Sean Davis
21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
A: Rtracklayer fails to export TxDb as GFF3 without CDS
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Store Matrix in DataFrame Cell
Store Matrix in DataFrame Cell
A: how to extract Granges not overlapping with other ganges?
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