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Batch
•
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4
votes
1
reply
1.1k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
luca.s
▴ 50
0
votes
1
reply
909
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 19 months ago by
Michael Love
41k • written 19 months ago by
estafana.t98
• 0
1
vote
7
replies
1.2k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
dequattro.concetta
▴ 10
0
votes
2
replies
994
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 2.2 years ago by
Steve Lianoglou
★ 13k • written 2.2 years ago by
Jonas
• 0
4
votes
7
replies
3.3k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 3.3 years ago by
Joana.silvestre
• 0 • written 4.6 years ago by
amin.ghareyazi
• 0
0
votes
1
reply
904
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.3 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
Katherine
• 0
0
votes
5
replies
1.7k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
Bine
▴ 40
1
vote
4
replies
1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.5 years ago by
davide risso
▴ 950 • written 3.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
4.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.6 years ago
Pietro
▴ 40
0
votes
2
replies
656
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
anshulmbi
• 0
0
votes
3
replies
918
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.1 years ago by
tmms
• 0 • written 4.1 years ago by
f_pardow
• 0
0
votes
1
reply
1.1k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
r.tom
• 0
3
votes
3
replies
957
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Solarion
• 0
6
votes
6
replies
1.5k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
english.server
▴ 20
10
votes
18
replies
16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.8 years ago
Mozart
▴ 30
0
votes
1
reply
750
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Mozart
▴ 30
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Pietro
▴ 40
0
votes
3
replies
922
views
DESEQ2 Batch effect
deseq2
batch
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
sherajilir
• 0
3
votes
3
replies
906
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
AZ
▴ 30
0
votes
4
replies
2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.4 years ago
j.viana
• 0
2
votes
1
reply
1.1k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Ekarl2
▴ 80
21 results • Page
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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
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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…
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