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0
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4
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2.5k
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DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.5 years ago
j.viana
• 0
3
votes
3
replies
946
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
AZ
▴ 30
0
votes
3
replies
957
views
DESEQ2 Batch effect
deseq2
batch
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
sherajilir
• 0
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
1
reply
774
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
42k • written 5.0 years ago by
Mozart
▴ 30
10
votes
18
replies
17k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
5.0 years ago • updated 4.9 years ago
Mozart
▴ 30
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
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
english.server
▴ 20
3
votes
3
replies
983
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
Solarion
• 0
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
42k • written 4.6 years ago by
r.tom
• 0
0
votes
3
replies
964
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
2
replies
687
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
anshulmbi
• 0
2
votes
8
replies
4.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.7 years ago
Pietro
▴ 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 3.6 years ago by
davide risso
▴ 950 • written 3.6 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
5
replies
1.8k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 3.6 years ago by
Michael Love
42k • written 3.6 years ago by
Bine
▴ 40
0
votes
1
reply
977
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
42k • written 20 months ago by
estafana.t98
• 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 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Ekarl2
▴ 80
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 2.4 years ago by
Jonas
• 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
4
votes
1
reply
1.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
luca.s
▴ 50
0
votes
1
reply
947
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
Katherine
• 0
21 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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