Showing : batch • reset
4
votes
1
reply
1.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
0
votes
1
reply
996
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 21 months ago by 42k • written 21 months ago by • 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
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 2.4 years ago by ★ 13k • written 2.4 years ago by • 0
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 • 0 • written 4.7 years ago by • 0
0
votes
1
reply
953
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by • 0
0
votes
5
replies
1.8k
views
DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 3.6 years ago by 42k • written 3.6 years ago by ▴ 40
1
vote
4
replies
1.8k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 3.7 years ago by ▴ 950 • written 3.7 years ago by ★ 1.5k
2
votes
8
replies
4.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
0
votes
2
replies
696
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
0
votes
3
replies
971
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 4.2 years ago by • 0 • written 4.3 years ago by • 0
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 42k • written 4.6 years ago by • 0
3
votes
3
replies
987
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 20
10
votes
18
replies
17k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
5.0 years ago Mozart ▴ 30
0
votes
1
reply
776
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 42k • written 5.0 years ago by ▴ 30
3
votes
5
replies
1.5k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 40
0
votes
3
replies
963
views
DESEQ2 Batch effect
deseq2 batch
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
3
votes
3
replies
953
views
Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 30
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.5 years ago j.viana • 0
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 ★ 28k • written 8.2 years ago by ▴ 80
21 results • Page 1 of 1
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Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by jane • 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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