Showing : batch • reset
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
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
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
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.5 years ago j.viana • 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
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
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
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
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
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
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
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
0
votes
1
reply
991
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
3
votes
3
replies
985
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 4.6 years ago by 42k • written 4.6 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 4.2 years ago by • 0
0
votes
3
replies
962
views
DESEQ2 Batch effect
deseq2 batch
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
1
reply
952
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
3
votes
3
replies
951
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
1
reply
775
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
0
votes
2
replies
690
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
21 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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