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removeBatchEffect
•
reset
4
votes
4
replies
810
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 weeks ago
sukeshinik5
• 0
0
votes
2
replies
1.0k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
18 months ago
dqt
• 0
0
votes
5
replies
4.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.5 years ago by
ATpoint
★ 4.2k • written 3.3 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
830
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 4.4 years ago by
Gordon Smyth
51k • written 4.4 years ago by
Sam
▴ 10
5
votes
7
replies
2.8k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.2 years ago
altintas.ali
• 0
1
vote
6
replies
1.8k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.2 years ago by
James W. MacDonald
66k • written 5.2 years ago by
Biologist
▴ 120
2
votes
5
replies
4.3k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
6.0 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.6k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 6.6 years ago by
Vladimir Kiselev
▴ 150 • written 6.6 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
11k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.9 years ago by
Gordon Smyth
51k • written 6.9 years ago by
lirongrossmann
▴ 80
9
votes
8
replies
9.0k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 6.9 years ago by
Gordon Smyth
51k • written 10.0 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.5k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
7.2 years ago
aina.jene
▴ 10
2
votes
2
replies
2.1k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 7.2 years ago by
sina.nassiri
▴ 130 • written 7.2 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.4k
views
Re-use limma beta coefficients
limma
removebatcheffect
7.7 years ago
Keifa
▴ 10
3
votes
6
replies
2.4k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.8 years ago by
Jakub
▴ 50 • written 7.8 years ago by
amoltej
▴ 10
0
votes
3
replies
1.4k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
Jenny Drnevich
★ 2.0k
17
votes
7
replies
6.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 8.2 years ago by
Ryan C. Thompson
★ 7.9k • written 8.2 years ago by
ompandey
▴ 10
4
votes
5
replies
2.7k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 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 8.5 years ago by
Bernd Klaus
▴ 610 • written 8.5 years ago by
Ekarl2
▴ 80
18 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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maltethodberg
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42k
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