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Batch
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4
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1
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192
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on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 7 weeks ago by
ATpoint
★ 2.3k • written 7 weeks ago by
luca.s
▴ 40
0
votes
1
reply
322
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 6 months ago by
Michael Love
39k • written 7 months ago by
estafana.t98
• 0
1
vote
7
replies
600
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 13 months ago by
James W. MacDonald
62k • written 13 months ago by
dequattro.concetta
▴ 10
0
votes
2
replies
641
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 14 months ago by
Steve Lianoglou
13k • written 14 months ago by
Jonas
• 0
4
votes
7
replies
2.4k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 2.3 years ago by
Joana.silvestre
• 0 • written 3.6 years ago by
amin.ghareyazi
• 0
0
votes
1
reply
546
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 2.3 years ago by
Kevin Blighe
3.8k • written 2.3 years ago by
Katherine
• 0
0
votes
5
replies
988
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 2.4 years ago by
Michael Love
39k • written 2.4 years ago by
Bine
▴ 20
1
vote
4
replies
1.0k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 2.5 years ago by
davide risso
▴ 920 • written 2.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
2.6k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
2.6 years ago
Pietro
▴ 40
0
votes
2
replies
372
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
anshulmbi
• 0
0
votes
3
replies
539
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 3.1 years ago by
tmms
• 0 • written 3.1 years ago by
f_pardow
• 0
0
votes
1
reply
750
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 3.5 years ago by
Michael Love
39k • written 3.5 years ago by
r.tom
• 0
3
votes
3
replies
659
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 3.5 years ago by
Michael Love
39k • written 3.5 years ago by
Solarion
• 0
6
votes
6
replies
1.0k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 3.5 years ago by
Gordon Smyth
47k • written 3.5 years ago by
english.server
▴ 20
6
votes
18
replies
11k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
3.8 years ago
Mozart
▴ 20
0
votes
1
reply
508
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
Mozart
▴ 20
3
votes
5
replies
920
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
Pietro
▴ 40
0
votes
3
replies
633
views
DESEQ2 Batch effect
deseq2
batch
updated 4.0 years ago by
Michael Love
39k • written 4.0 years ago by
sherajilir
• 0
3
votes
3
replies
688
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 4.2 years ago by
Michael Love
39k • written 4.2 years ago by
AZ
▴ 30
0
votes
4
replies
2.0k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
6.3 years ago
j.viana
• 0
2
votes
1
reply
847
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Ekarl2
▴ 80
21 results • Page
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Hi, I came across the same issue when trying to install `msa` in a docker (singularity) container. My base image was `debian:bullseye-20230…
Comment: deseq2 nested multifactorial analysis
by
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▴ 700
The information on genotype is included in the condition : all Control_1 are A, all Control_2 are B The condition variable is sufficient to…
Comment: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
by
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▴ 10
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Rory Stark
★ 4.6k
`dba.count()` counts reads overlapping consensus regions. After that, the original peak scores are ignored. All quantitative analysis (via …
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I'd like to test: 1. Are there differences between treatment (cold vs regrowth) time profiles for each line? 2. Do lines react differentl…
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