Showing : batch • reset
4
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1.6k
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on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 50
0
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1
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1.4k
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
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7
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1.7k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.8 years ago by 67k • written 2.8 years ago by ▴ 10
0
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2
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1.2k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.9 years ago by ★ 13k • written 2.9 years ago by • 0
5
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7
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3.9k
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DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 4.0 years ago by • 0 • written 5.3 years ago by • 0
0
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1
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1.2k
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Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
0
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5
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2.2k
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DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 50
1
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4
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2.2k
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How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 4.2 years ago by ▴ 980 • written 4.2 years ago by ★ 1.5k
2
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8
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5.0k
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Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.3 years ago Pietro ▴ 40
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2
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900
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DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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3
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1.2k
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Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 4.8 years ago by • 0 • written 4.8 years ago by • 0
0
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1
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1.4k
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Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
3
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3
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1.1k
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DESeq2 indirect batch effect removal
deseq2 batch
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
6
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6
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1.8k
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Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 5.2 years ago by 52k • written 5.2 years ago by ▴ 20
10
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20
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21k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 8 weeks ago by 67k • written 5.5 years ago by ▴ 30
0
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1
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916
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DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
3
votes
5
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1.7k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 40
0
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3
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1.1k
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DESEQ2 Batch effect
deseq2 batch
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
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3
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1.1k
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Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 30
0
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4
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2.8k
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DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
8.1 years ago j.viana • 0
2
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1
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1.3k
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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 ★ 28k • written 8.8 years ago by ▴ 80
21 results • Page 1 of 1
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Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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