Showing : removebatcheffect • reset
2
votes
2
replies
363
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
3 months ago sukeshinik5 ▴ 20
17
votes
9
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7.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 3 months ago by 67k • written 8.6 years ago by ▴ 10
4
votes
4
replies
1.2k
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
6 months ago sukeshinik5 ▴ 20
0
votes
2
replies
1.3k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
24 months ago dqt • 0
0
votes
5
replies
4.7k
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
975
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
5.6 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 5.6 years ago by 67k • written 5.6 years ago by ▴ 120
2
votes
5
replies
4.6k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.4 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 7.3 years ago by 52k • written 7.3 years ago by ▴ 80
9
votes
8
replies
9.9k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 7.3 years ago by 52k • written 10.4 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
7.6 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 7.6 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
8.1 years ago Keifa ▴ 10
3
votes
6
replies
2.8k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 8.2 years ago by ▴ 50 • written 8.2 years ago by ▴ 10
0
votes
3
replies
1.6k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ★ 2.0k
4
votes
5
replies
2.9k
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: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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