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4
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1
answer
428
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1
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sva combat removes wanted biological variation
R sva combat rna-seq pca written 10 months ago by exin • 50 • updated 20 days ago by Biostar ♦♦ 20
0
votes
0
answers
86
views
0
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In SVA, the percent of biological variable of interest didnot change after adding SV1.
R sva combat written 5 weeks ago by dhwani2410 • 0 • updated 5 weeks ago by Kevin Blighe ♦ 52k
3
votes
1
answer
147
views
1
answer
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 3 months ago by rodguinea • 0 • updated 3 months ago by i.sudbery ♦ 6.3k
2
votes
1
answer
249
views
1
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Remove batch effect for many RNA-seq
sva combat rna-seq batch effect written 4 months ago by Shaway • 0
0
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0
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192
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0
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Strong covariates and weak biological signal in transcriptomes
R sva written 6 months ago by Agustin Gonzalez-Vicente • 50 • updated 5 months ago by zx8754 ♦ 8.7k
6
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1
answer
291
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1
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pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"
R bioconductor pvca sva pdata written 6 months ago by RNAseqer • 110 • updated 6 months ago by zx8754 ♦ 8.7k
2
votes
1
answer
329
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1
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Principal component analysis of SVA's surrogate variables
sva stdev surrogate variables written 6 months ago by RNAseqer • 110 • updated 6 months ago by geek_y ♦ 10k
0
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0
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245
views
0
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contrast matrix design question, limma-sva
sva contrast matrix limma written 7 months ago by RNAseqer • 110
0
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0
answers
170
views
0
answers
sva pprob.b all 0s?
R sva pprob.b microarray written 7 months ago by RNAseqer • 110
3
votes
1
answer
517
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1
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Using SVA to correct for covariates in RNA-seq data
R sva corrections covariates rna-seq written 8 months ago by sbrown669 • 20
0
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0
answers
414
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0
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Question about sva + edgeR to identify differentially expressed genes
sva edger written 8 months ago by tujuchuanli • 50 • updated 8 months ago by ATpoint ♦ 26k
0
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0
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2.0k
views
0
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svaseq and combat
combat sva effect batch written 2.6 years ago by Folder40g • 120 • updated 8 months ago by liull_hust • 0
12
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1
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13k
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1
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removing batch effects using ComBat and SVA
R sva combat batch effect written 3.5 years ago by LJ • 180 • updated 10 months ago by Agustin Gonzalez-Vicente • 50
0
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0
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230
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0
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sva correction for MEDIPS
medip-seq sva svaseq medips written 10 months ago by tofukaj • 0
0
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0
answers
400
views
0
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ComBat correction with one batch containing only one sample - keep or remove?
proteome sva combat R written 12 months ago by hesse.sebastian • 80 • updated 10 months ago by Biostar ♦♦ 20
1
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0
answers
344
views
0
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Normalise batch effects for Percent Spliced In (PSI) matrice
sva combat splicing written 10 months ago by ZheFrench • 270
3
votes
1
answer
444
views
5 follow
1
answer
sva output interpretation
sva rna-seq written 14 months ago by elb • 170 • updated 14 months ago by Devon Ryan ♦ 93k
6
votes
1
answer
1.3k
views
1
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Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
R sva deseq2 batch effects written 15 months ago by Kristin Muench • 470 • updated 15 months ago by Teresa • 20
1
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1
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1.3k
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1
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Help with multiple batch effects
sva batch effects combat written 17 months ago by fp89 • 20 • updated 17 months ago by genomax ♦ 75k
0
votes
0
answers
343
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0
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how to combine sva with survival analysis to validate genes in an independent dataset?
coxph sva coxnet survival rna-seq written 17 months ago by a.e.c • 30
1
vote
1
answer
644
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1
answer
Batch effect correction
sva combat matlab written 18 months ago by gstavropoulos1991 • 10
1
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0
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774
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0
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SVA Input: Should SVs be calculated on normalized data?
R sva rna-seq written 18 months ago by Kristin Muench • 470
6
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1
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1.0k
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5 follow
1
answer
Surrogate variable analysis: ask for a practical example
sva rna-seq written 19 months ago by Mozart • 140 • updated 19 months ago by RamRS ♦ 25k
3
votes
1
answer
935
views
1
answer
RNAseq sva-seq drops number of DE genes?
R sva svaseq rna-seq written 19 months ago by brismiller • 10 • updated 19 months ago by Kevin Blighe ♦ 52k
0
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0
answers
1.1k
views
0
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Can't make sva comparison despite very distinct batch effects
sva factors batch effect written 21 months ago by jjrin • 10
1
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0
answers
1.1k
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0
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Plotting a PCA Plot from SVASeq results
pca plot sva batch effects svaseq ruvseq written 22 months ago by jjrin • 10
18
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1
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11k
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14 follow
1
answer
Batch effects : ComBat or removebatcheffects (limma package) ?
sva batch effects combat limma written 2.3 years ago by lessismore • 710 • updated 2.1 years ago by Kevin Blighe ♦ 52k
7
votes
1
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2.0k
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6 follow
1
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RNA-Seq Batch correction negative values
batch-effect combat scran rna-seq sva written 2.2 years ago by rmf • 750 • updated 2.2 years ago by Kevin Blighe ♦ 52k
10
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0
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3.5k
views
6 follow
0
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SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva batch effects combat written 2.4 years ago by lessismore • 710 • updated 2.2 years ago by Biostar ♦♦ 20
0
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1
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1.4k
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1
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SVA analysis output R
R sva rna-seq written 2.2 years ago by robertt_bw • 0 • updated 2.2 years ago by lessismore • 710
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