Showing : removeBatchEffect • reset
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 9.2 years ago by ▴ 610 • written 9.2 years ago by ▴ 80
17
votes
9
replies
7.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6 months ago by 68k • written 8.8 years ago by ▴ 10
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
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
5
votes
7
replies
3.3k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
5.8 years ago altintas.ali • 0
1
vote
6
replies
2.1k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 120
3
votes
6
replies
3.0k
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
4
votes
5
replies
3.1k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 9.1 years ago by ★ 28k • written 9.1 years ago by ▴ 10
2
votes
5
replies
4.9k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.7 years ago Antonio Ahn ▴ 10
0
votes
5
replies
5.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.2 years ago by ★ 4.8k • written 4.0 years ago by • 0
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
9 months ago sukeshinik5 ▴ 20
1
vote
3
replies
1.6k
views
Re-use limma beta coefficients
limma removebatcheffect
8.3 years ago Keifa ▴ 10
0
votes
3
replies
1.7k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ★ 2.0k
0
votes
2
replies
1.4k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.2 years ago dqt • 0
2
votes
2
replies
2.4k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 7.9 years ago by ▴ 130 • written 7.9 years ago by ▴ 10
2
votes
2
replies
487
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
6 months ago sukeshinik5 ▴ 20
0
votes
1
reply
1.0k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 5.1 years ago by 52k • written 5.1 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.3 years ago by ▴ 150 • written 7.3 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva R removebatcheffect
7.9 years ago aina.jene ▴ 10
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Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Mike Smith ★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
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The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
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Ideally you would have S4 methods that dispatch on the incoming data structure, so people could call your main function using a `data.frame…
Comment: ComBat with repeated measures by ATpoint ★ 4.8k
It looks to me that you do not need the batch information since subject is nested with batch so correcting for subject will do a paired ana…
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