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Batch
•
reset
4
votes
1
reply
1.9k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 2.3 years ago by
ATpoint
★ 4.8k • written 2.3 years ago by
luca.s
▴ 50
0
votes
1
reply
1.6k
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
estafana.t98
• 0
1
vote
7
replies
2.0k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
dequattro.concetta
▴ 10
0
votes
2
replies
1.3k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 3.3 years ago by
Steve Lianoglou
★ 13k • written 3.3 years ago by
Jonas
• 0
6
votes
7
replies
4.3k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 4.4 years ago by
Joana.silvestre
• 0 • written 5.7 years ago by
amin.ghareyazi
• 0
0
votes
1
reply
1.3k
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
Katherine
• 0
0
votes
5
replies
2.5k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Bine
▴ 50
1
vote
4
replies
2.6k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 4.6 years ago by
davide risso
▴ 980 • written 4.6 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
5.6k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
4.7 years ago
Pietro
▴ 40
0
votes
2
replies
1.0k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
anshulmbi
• 0
0
votes
3
replies
1.4k
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 5.2 years ago by
tmms
• 0 • written 5.2 years ago by
f_pardow
• 0
0
votes
1
reply
1.5k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
r.tom
• 0
3
votes
3
replies
1.2k
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
Solarion
• 0
6
votes
6
replies
2.0k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 5.6 years ago by
Gordon Smyth
52k • written 5.6 years ago by
english.server
▴ 20
10
votes
20
replies
25k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
updated 6 months ago by
James W. MacDonald
68k • written 5.9 years ago by
Mozart
▴ 30
0
votes
1
reply
1.0k
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
Mozart
▴ 30
3
votes
5
replies
1.8k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Pietro
▴ 40
0
votes
3
replies
1.2k
views
DESEQ2 Batch effect
deseq2
batch
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
sherajilir
• 0
3
votes
3
replies
1.1k
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
AZ
▴ 30
0
votes
4
replies
3.0k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
8.5 years ago
j.viana
• 0
2
votes
1
reply
1.4k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 9.2 years ago by
Aaron Lun
★ 28k • written 9.2 years ago by
Ekarl2
▴ 80
21 results • Page
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Comment: Design formula for circadian time-course data for vst() function
by
Vishnu
• 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2
by
Tom
• 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function
by
ATpoint
★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Comment: Module membership vs gene significance result and Modules-trait relationships re
by
Vinaya
• 0
Hi. I am having the same issue, and haven't found a solution still.
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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