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removeBatchEffect
•
reset
0
votes
2
replies
858
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
14 months ago
dqt
• 0
0
votes
5
replies
3.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.2 years ago by
ATpoint
★ 4.0k • written 3.0 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
739
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect
limma
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
Sam
▴ 10
5
votes
7
replies
2.5k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
4.8 years ago
altintas.ali
• 0
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
Biologist
▴ 110
2
votes
5
replies
4.1k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
5.7 years ago
Antonio Ahn
▴ 10
1
vote
1
reply
1.5k
views
Batch effect removal before SC3?
SC3
batch effect
removebatcheffect
updated 6.3 years ago by
Vladimir Kiselev
▴ 150 • written 6.3 years ago by
muad.abdelhay
▴ 10
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
lirongrossmann
▴ 80
0
votes
1
reply
2.3k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva
R
removebatcheffect
6.9 years ago
aina.jene
▴ 10
2
votes
2
replies
2.0k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva
removebatcheffect
R
updated 6.9 years ago by
sina.nassiri
▴ 130 • written 6.9 years ago by
aina.jene
▴ 10
1
vote
3
replies
1.2k
views
Re-use limma beta coefficients
limma
removebatcheffect
7.3 years ago
Keifa
▴ 10
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.4 years ago by
Jakub
▴ 50 • written 7.4 years ago by
amoltej
▴ 10
0
votes
3
replies
1.3k
views
How to remove nested batch effects with removeBatchEffect?
edgeR
removeBatchEffect
nested design
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
Jenny Drnevich
★ 2.0k
17
votes
7
replies
5.7k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
ompandey
▴ 10
4
votes
5
replies
2.6k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 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 8.2 years ago by
Bernd Klaus
▴ 610 • written 8.2 years ago by
Ekarl2
▴ 80
9
votes
8
replies
8.4k
views
removeBatchEffect options: design and covariates
limma
removebatcheffect
updated 6.5 years ago by
Gordon Smyth
50k • written 9.6 years ago by
Rao,Xiayu
▴ 550
17 results • Page
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Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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