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3
votes
1
answer
82
views
1
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Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
sva batch effects combat rna-seq cross-species written 17 days ago by rodguinea • 0 • updated 17 days ago by i.sudbery ♦ 5.3k
2
votes
0
answers
173
views
0
answers
Remove batch effect for many RNA-seq
sva combat rna-seq batch effect written 9 weeks ago by Shaway • 0
0
votes
0
answers
163
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0
answers
Strong covariates and weak biological signal in transcriptomes
R sva written 3 months ago by Agustin Gonzalez-Vicente • 40 • updated 3 months ago by zx8754 ♦ 8.2k
6
votes
1
answer
223
views
1
answer
pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"
R bioconductor pvca sva pdata written 4 months ago by RNAseqer • 110 • updated 4 months ago by zx8754 ♦ 8.2k
2
votes
1
answer
224
views
1
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Principal component analysis of SVA's surrogate variables
sva stdev surrogate variables written 4 months ago by RNAseqer • 110 • updated 4 months ago by geek_y ♦ 9.9k
0
votes
0
answers
182
views
0
answers
contrast matrix design question, limma-sva
sva contrast matrix limma written 4 months ago by RNAseqer • 110
0
votes
0
answers
129
views
0
answers
sva pprob.b all 0s?
R sva pprob.b microarray written 4 months ago by RNAseqer • 110
3
votes
1
answer
413
views
1
answer
Using SVA to correct for covariates in RNA-seq data
R sva corrections covariates rna-seq written 6 months ago by sbrown669 • 20
0
votes
0
answers
305
views
0
answers
Question about sva + edgeR to identify differentially expressed genes
sva edger written 5 months ago by tujuchuanli • 50 • updated 5 months ago by ATpoint ♦ 23k
0
votes
0
answers
1.8k
views
0
answers
svaseq and combat
combat sva effect batch written 2.3 years ago by Folder40g • 120 • updated 6 months ago by liull_hust • 0
12
votes
1
answer
12k
views
1
answer
removing batch effects using ComBat and SVA
R sva combat batch effect written 3.3 years ago by LJ • 180 • updated 7 months ago by Agustin Gonzalez-Vicente • 40
4
votes
0
answers
351
views
0
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sva combat removes wanted biological variation
R sva combat rna-seq pca written 7 months ago by exin • 50 • updated 7 months ago by zx8754 ♦ 8.2k
0
votes
0
answers
193
views
0
answers
sva correction for MEDIPS
medip-seq sva svaseq medips written 7 months ago by tofukaj • 0
0
votes
0
answers
338
views
0
answers
ComBat correction with one batch containing only one sample - keep or remove?
proteome sva combat R written 10 months ago by hesse.sebastian • 80 • updated 8 months ago by Biostar ♦♦ 20
1
vote
0
answers
287
views
0
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Normalise batch effects for Percent Spliced In (PSI) matrice
sva combat splicing written 8 months ago by ZheFrench • 250
3
votes
1
answer
382
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5 follow
1
answer
sva output interpretation
sva rna-seq written 11 months ago by elb • 160 • updated 11 months ago by Devon Ryan ♦ 92k
6
votes
1
answer
1.1k
views
1
answer
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
R sva deseq2 batch effects written 13 months ago by Kristin Muench • 450 • updated 12 months ago by Teresa • 20
1
vote
1
answer
1.1k
views
1
answer
Help with multiple batch effects
sva batch effects combat written 14 months ago by fp89 • 20 • updated 14 months ago by genomax ♦ 71k
0
votes
0
answers
311
views
0
answers
how to combine sva with survival analysis to validate genes in an independent dataset?
coxph sva coxnet survival rna-seq written 14 months ago by a.e.c • 30
1
vote
1
answer
579
views
1
answer
Batch effect correction
sva combat matlab written 16 months ago by gstavropoulos1991 • 10
1
vote
0
answers
676
views
0
answers
SVA Input: Should SVs be calculated on normalized data?
R sva rna-seq written 16 months ago by Kristin Muench • 450
6
votes
1
answer
952
views
5 follow
1
answer
Surrogate variable analysis: ask for a practical example
sva rna-seq written 17 months ago by Mozart • 140 • updated 17 months ago by RamRS ♦ 24k
2
votes
1
answer
841
views
1
answer
RNAseq sva-seq drops number of DE genes?
R sva svaseq rna-seq written 17 months ago by brismiller • 10 • updated 17 months ago by Kevin Blighe ♦ 48k
0
votes
0
answers
993
views
0
answers
Can't make sva comparison despite very distinct batch effects
sva factors batch effect written 19 months ago by jjrin • 10
1
vote
0
answers
998
views
0
answers
Plotting a PCA Plot from SVASeq results
pca plot sva batch effects svaseq ruvseq written 19 months ago by jjrin • 10
17
votes
1
answer
9.2k
views
14 follow
1
answer
Batch effects : ComBat or removebatcheffects (limma package) ?
sva batch effects combat limma written 2.1 years ago by lessismore • 690 • updated 23 months ago by Kevin Blighe ♦ 48k
7
votes
1
answer
1.8k
views
6 follow
1
answer
RNA-Seq Batch correction negative values
batch-effect combat scran rna-seq sva written 24 months ago by rmf • 730 • updated 24 months ago by Kevin Blighe ♦ 48k
10
votes
0
answers
3.1k
views
6 follow
0
answers
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva batch effects combat written 2.2 years ago by lessismore • 690 • updated 2.0 years ago by Biostar ♦♦ 20
0
votes
1
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1.3k
views
1
answer
SVA analysis output R
R sva rna-seq written 2.0 years ago by robertt_bw • 0 • updated 2.0 years ago by lessismore • 690
1
vote
2
answers
1.1k
views
2
answers
Taking surrogate variable into account before running PCA
sva svaseq batch effect written 2.3 years ago by wamiqsaifi • 0 • updated 2.2 years ago by ivivek_ngs • 4.8k
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