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Showing :
batch
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4
votes
1
reply
637
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on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 7 months ago by
ATpoint
★ 3.4k • written 7 months ago by
luca.s
▴ 50
0
votes
1
reply
617
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 13 months ago by
Michael Love
40k • written 13 months ago by
estafana.t98
• 0
1
vote
7
replies
889
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 19 months ago by
James W. MacDonald
63k • written 19 months ago by
dequattro.concetta
▴ 10
0
votes
2
replies
803
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 20 months ago by
Steve Lianoglou
13k • written 21 months ago by
Jonas
• 0
4
votes
7
replies
2.9k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 2.8 years ago by
Joana.silvestre
• 0 • written 4.1 years ago by
amin.ghareyazi
• 0
0
votes
1
reply
726
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 2.8 years ago by
Kevin Blighe
3.8k • written 2.8 years ago by
Katherine
• 0
0
votes
5
replies
1.3k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 2.9 years ago by
Michael Love
40k • written 2.9 years ago by
Bine
▴ 20
1
vote
4
replies
1.4k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.0 years ago by
davide risso
▴ 920 • written 3.0 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
3.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.1 years ago
Pietro
▴ 40
0
votes
2
replies
496
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 3.5 years ago by
Michael Love
40k • written 3.5 years ago by
anshulmbi
• 0
0
votes
3
replies
721
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 3.6 years ago by
tmms
• 0 • written 3.6 years ago by
f_pardow
• 0
0
votes
1
reply
971
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
r.tom
• 0
3
votes
3
replies
806
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
Solarion
• 0
6
votes
6
replies
1.3k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.0 years ago by
Gordon Smyth
48k • written 4.0 years ago by
english.server
▴ 20
6
votes
18
replies
13k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.3 years ago
Mozart
▴ 20
0
votes
1
reply
641
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 4.4 years ago by
Michael Love
40k • written 4.4 years ago by
Mozart
▴ 20
3
votes
5
replies
1.1k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
Pietro
▴ 40
0
votes
3
replies
786
views
DESEQ2 Batch effect
deseq2
batch
updated 4.5 years ago by
Michael Love
40k • written 4.5 years ago by
sherajilir
• 0
3
votes
3
replies
780
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 4.7 years ago by
Michael Love
40k • written 4.7 years ago by
AZ
▴ 30
0
votes
4
replies
2.3k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
6.9 years ago
j.viana
• 0
2
votes
1
reply
947
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
Ekarl2
▴ 80
21 results • Page
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Comment: DMRcate design
by
James W. MacDonald
63k
That's what identical context means.
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2
by
jd774
• 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
Answer: heatmap.2 - change column & row locations; angle / rotate
by
nehagoyal6397
• 0
Window 10 are comes with the new updates [how to fix connections to wireless displays in windows 10](http://fixwindows10connections.com) ju…
Comment: filtering out lowly expressed genes by groups
by
James W. MacDonald
63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
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