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4
Votes
7
Replies
769
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DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
17 months ago
amin.ghareyazi
• 0
• updated 5 weeks ago
Joana.silvestre
• 0
0
Votes
1
Reply
55
Views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
7 weeks ago
Katherine
• 0
• updated 7 weeks ago
Kevin Blighe
2.3k
0
Votes
5
Replies
118
Views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
12 weeks ago
Bine
• 0
• updated 12 weeks ago
Michael Love
31k
1
Vote
4
Replies
118
Views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
4 months ago
Assa Yeroslaviz
♦ 1.5k
• updated 4 months ago
davide risso
• 850
2
Votes
8
Replies
293
Views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
5 months ago
Pietro
• 30
0
Votes
2
Replies
46
Views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
9 months ago
anshulmbi
• 0
• updated 9 months ago
Michael Love
31k
0
Votes
3
Replies
162
Views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
11 months ago
f_pardow
• 0
• updated 11 months ago
tmms
• 0
0
Votes
1
Reply
188
Views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
15 months ago
r.tom
• 0
• updated 15 months ago
Michael Love
31k
3
Votes
3
Replies
186
Views
DESeq2 indirect batch effect removal
deseq2
batch
15 months ago
Solarion
• 0
• updated 15 months ago
Michael Love
31k
6
Votes
6
Replies
276
Views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
16 months ago
english.server
• 20
• updated 16 months ago
Gordon Smyth
41k
5
Votes
18
Replies
4.1k
Views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
20 months ago • updated 19 months ago
Mozart
• 10
0
Votes
1
Reply
196
Views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
20 months ago
Mozart
• 10
• updated 20 months ago
Michael Love
31k
3
Votes
5
Replies
362
Views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
22 months ago
Pietro
• 30
• updated 22 months ago
Aaron Lun
♦ 26k
0
Votes
3
Replies
222
Views
DESEQ2 Batch effect
deseq2
batch
22 months ago
sherajilir
• 0
• updated 22 months ago
Michael Love
31k
3
Votes
3
Replies
405
Views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
2.0 years ago
Fereshteh
• 20
• updated 2.0 years ago
Michael Love
31k
0
Votes
4
Replies
1.2k
Views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
4.2 years ago
j.viana
• 0
2
Votes
1
Reply
622
Views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
4.9 years ago
Ekarl2
• 70
• updated 4.9 years ago
Aaron Lun
♦ 26k
17 results • Page
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Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE
by
Pedram
• 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in
by
Konstantinos Yeles
• 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package
by
shrinka.genetics
• 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker
by
Konstantinos Yeles
• 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to anal
by
larissa.stanberry
• 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
Votes
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
DEXSeq Usage and Expression Confusion
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