Showing : removeBatchEffect • reset
2
votes
2
replies
387
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
4 months ago sukeshinik5 ▴ 20
17
votes
9
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7.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 4 months ago by 67k • written 8.7 years ago by ▴ 10
4
votes
4
replies
1.3k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
7 months ago sukeshinik5 ▴ 20
0
votes
2
replies
1.3k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.1 years ago dqt • 0
0
votes
5
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4.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.0 years ago by ★ 4.6k • written 3.8 years ago by • 0
0
votes
1
reply
987
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 4.9 years ago by 52k • written 4.9 years ago by ▴ 10
5
votes
7
replies
3.1k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
5.7 years ago altintas.ali • 0
1
vote
6
replies
2.0k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 120
2
votes
5
replies
4.7k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.5 years ago Antonio Ahn ▴ 10
1
vote
1
reply
1.8k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.4 years ago by 52k • written 7.4 years ago by ▴ 80
9
votes
8
replies
10k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 7.4 years ago by 52k • written 10.5 years ago by ▴ 550
0
votes
1
reply
2.7k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva R removebatcheffect
7.7 years ago aina.jene ▴ 10
2
votes
2
replies
2.3k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 7.7 years ago by ▴ 130 • written 7.7 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Re-use limma beta coefficients
limma removebatcheffect
8.2 years ago Keifa ▴ 10
3
votes
6
replies
2.9k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 8.3 years ago by ▴ 50 • written 8.3 years ago by ▴ 10
0
votes
3
replies
1.6k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ★ 2.0k
4
votes
5
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3.0k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 10
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma removeBatchEffect heatmap clustering
updated 9.0 years ago by ▴ 610 • written 9.0 years ago by ▴ 80
19 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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