Showing : batch • reset
4
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1.2k
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on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 50
0
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1
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942
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
1
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7
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1.2k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
0
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2
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1.0k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.3 years ago by ★ 13k • written 2.3 years ago by • 0
4
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7
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3.4k
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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
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1
reply
927
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Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
0
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5
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1.7k
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DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
1
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4
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1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 3.6 years ago by ▴ 950 • written 3.6 years ago by ★ 1.5k
2
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8
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4.2k
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Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
0
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2
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671
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DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
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3
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944
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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
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1
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1.2k
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Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
3
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3
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973
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
6
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6
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1.6k
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Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
10
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18
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16k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
4.9 years ago Mozart ▴ 30
0
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1
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762
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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 41k • written 5.0 years ago by ▴ 30
3
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5
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1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
0
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3
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938
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DESEQ2 Batch effect
deseq2 batch
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
3
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3
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922
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Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 30
0
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4
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2.5k
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DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.4 years ago j.viana • 0
2
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1
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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: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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