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batch
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10
votes
18
replies
16k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.9 years ago
Mozart
▴ 30
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.7 years ago
Pietro
▴ 40
4
votes
7
replies
3.4k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 3.4 years ago by
Joana.silvestre
• 0 • written 4.7 years ago by
amin.ghareyazi
• 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
dequattro.concetta
▴ 10
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
english.server
▴ 20
0
votes
5
replies
1.7k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
Bine
▴ 40
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Pietro
▴ 40
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
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 3.6 years ago by
davide risso
▴ 950 • written 3.6 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
3
replies
976
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
Solarion
• 0
3
votes
3
replies
931
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
AZ
▴ 30
0
votes
3
replies
950
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.2 years ago by
tmms
• 0 • written 4.2 years ago by
f_pardow
• 0
0
votes
3
replies
940
views
DESEQ2 Batch effect
deseq2
batch
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
sherajilir
• 0
0
votes
2
replies
677
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
anshulmbi
• 0
0
votes
2
replies
1.0k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 2.3 years ago by
Steve Lianoglou
★ 13k • written 2.3 years ago by
Jonas
• 0
0
votes
1
reply
948
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
estafana.t98
• 0
0
votes
1
reply
766
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
Mozart
▴ 30
0
votes
1
reply
1.2k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
r.tom
• 0
0
votes
1
reply
934
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
Katherine
• 0
4
votes
1
reply
1.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
luca.s
▴ 50
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 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Ekarl2
▴ 80
21 results • Page
1 of 1
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Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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