Showing : removeBatchEffect • reset
2
votes
6
replies
2.9k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
4 months ago • updated 3 months ago massimo • 0
2
votes
2
replies
691
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
11 months ago sukeshinik5 ▴ 20
17
votes
9
replies
8.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 12 months ago by 68k • written 9.3 years ago by ▴ 10
4
votes
4
replies
1.6k
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
14 months ago sukeshinik5 ▴ 20
0
votes
2
replies
1.6k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.7 years ago dqt • 0
0
votes
5
replies
5.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.7 years ago by ★ 4.9k • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 10
5
votes
7
replies
3.5k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
6.3 years ago altintas.ali • 0
1
vote
6
replies
2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 120
2
votes
5
replies
5.3k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
7.1 years ago Antonio Ahn ▴ 10
1
vote
1
reply
2.0k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.8 years ago by ▴ 150 • written 7.8 years ago by ▴ 10
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 80
9
votes
8
replies
11k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 8.0 years ago by 53k • written 11.1 years ago by ▴ 550
0
votes
1
reply
2.9k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva R removebatcheffect
8.3 years ago aina.jene ▴ 10
2
votes
2
replies
2.6k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 8.4 years ago by ▴ 130 • written 8.4 years ago by ▴ 10
1
vote
3
replies
1.7k
views
Re-use limma beta coefficients
limma removebatcheffect
8.8 years ago Keifa ▴ 10
3
votes
6
replies
3.3k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 8.9 years ago by ▴ 50 • written 8.9 years ago by ▴ 10
0
votes
3
replies
1.8k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ★ 2.0k
4
votes
5
replies
3.3k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 9.6 years ago by ★ 29k • written 9.6 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 9.7 years ago by ▴ 610 • written 9.7 years ago by ▴ 80
20 results • Page 1 of 1
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Replies
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It is not uncommon for library size to be apparent in an MDS plot. You can use `sva` or `RUV` to account for that.
Comment: p-adjusted values in multiple comparisons by Josh • 0
Yes, using lmFit with block and duplicateCorrelation is appropriate; mobile data collection can illustrate blocking importance. First estim…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Understood, thanks. The issue I'm seeing is that even after normalization, the MDSplot still orders samples by library size. I suspect cell…
Votes
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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