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batch
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10
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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
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
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
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
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
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
933
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
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
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
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
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
1
reply
956
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
4
replies
2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.4 years ago
j.viana
• 0
0
votes
3
replies
942
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
1
reply
770
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
3
replies
953
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
678
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
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
0
votes
1
reply
936
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
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
21 results • Page
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Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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