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Batch
•
reset
4
votes
1
reply
1.6k
views
on which data type limma::removeBatchEffect can be applyed?
batch
limma
updated 23 months ago by
ATpoint
★ 4.6k • written 23 months ago by
luca.s
▴ 50
0
votes
1
reply
1.4k
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
estafana.t98
• 0
1
vote
7
replies
1.7k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.8 years ago by
James W. MacDonald
67k • written 2.8 years ago by
dequattro.concetta
▴ 10
0
votes
2
replies
1.2k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 3.0 years ago by
Steve Lianoglou
★ 13k • written 3.0 years ago by
Jonas
• 0
5
votes
7
replies
3.9k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2
comparison
batch
updated 4.0 years ago by
Joana.silvestre
• 0 • written 5.3 years ago by
amin.ghareyazi
• 0
0
votes
1
reply
1.2k
views
Limma: Correct for location and batch effect
limma
BatchEffect
duplicatecorrelation
block
batch
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
Katherine
• 0
0
votes
5
replies
2.2k
views
DeSeq2 with three batches - Remove batch Effect
deseq2
batch
removebatch effect
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
Bine
▴ 50
1
vote
4
replies
2.2k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 4.3 years ago by
davide risso
▴ 980 • written 4.3 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
8
replies
5.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
4.3 years ago
Pietro
▴ 40
0
votes
2
replies
915
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
anshulmbi
• 0
0
votes
3
replies
1.2k
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.8 years ago by
tmms
• 0 • written 4.8 years ago by
f_pardow
• 0
0
votes
1
reply
1.4k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
r.tom
• 0
3
votes
3
replies
1.1k
views
DESeq2 indirect batch effect removal
deseq2
batch
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Solarion
• 0
6
votes
6
replies
1.9k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 5.3 years ago by
Gordon Smyth
52k • written 5.3 years ago by
english.server
▴ 20
10
votes
20
replies
22k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
updated 11 weeks ago by
James W. MacDonald
67k • written 5.6 years ago by
Mozart
▴ 30
0
votes
1
reply
926
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
Mozart
▴ 30
3
votes
5
replies
1.7k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Pietro
▴ 40
0
votes
3
replies
1.1k
views
DESEQ2 Batch effect
deseq2
batch
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
sherajilir
• 0
3
votes
3
replies
1.1k
views
Correcting the batch effect in Edgeseq data
DESeq2
Edgeseq
batch
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
AZ
▴ 30
0
votes
4
replies
2.9k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
8.1 years ago
j.viana
• 0
2
votes
1
reply
1.3k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq
edgeR
limma
removebatcheffect()
batch
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Ekarl2
▴ 80
21 results • Page
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Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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