Showing : removebatcheffect • reset
2
votes
2
replies
442
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
5 months ago sukeshinik5 ▴ 20
17
votes
9
replies
7.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 5 months ago by 68k • written 8.8 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
8 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
replies
5.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.1 years ago by ★ 4.7k • written 3.9 years ago by • 0
0
votes
1
reply
1.0k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 5.0 years ago by 52k • written 5.0 years ago by ▴ 10
5
votes
7
replies
3.2k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
5.8 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 5.8 years ago by 68k • written 5.8 years ago by ▴ 120
2
votes
5
replies
4.8k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.6 years ago Antonio Ahn ▴ 10
1
vote
1
reply
1.8k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ▴ 10
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 80
9
votes
8
replies
10k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 7.5 years ago by 52k • written 10.6 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
7.8 years ago aina.jene ▴ 10
2
votes
2
replies
2.4k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by ▴ 10
1
vote
3
replies
1.6k
views
Re-use limma beta coefficients
limma removebatcheffect
8.3 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 8.4 years ago by ▴ 50 • written 8.4 years ago by ▴ 10
0
votes
3
replies
1.7k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ★ 2.0k
4
votes
5
replies
3.0k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 9.0 years ago by ★ 28k • written 9.0 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 9.1 years ago by ▴ 610 • written 9.1 years ago by ▴ 80
19 results • Page 1 of 1
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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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