Showing : sva • reset
0
votes
3
replies
247
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 27 days ago by • 0
0
votes
0
replies
348
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
8 months ago dudwnsrla1 • 0
0
votes
1
reply
782
views
Combat-seq usage
sva
8 months ago • updated 7 months ago bbao ▴ 10
0
votes
0
replies
420
views
Batch correction for microarray
BatchEffect sva MicroarrayData
9 months ago Shaimaa Gamal • 0
1
vote
1
reply
1.1k
views
ComBat with repeated measures
ComBat sva
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
3
votes
5
replies
1.7k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
11 months ago bbao ▴ 10
0
votes
2
replies
999
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 13 months ago by 53k • written 13 months ago by ▴ 10
0
votes
3
replies
1.3k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
15 months ago Travis • 0
4
votes
5
replies
13k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 17 months ago by • 0 • written 8.3 years ago by ▴ 60
0
votes
4
replies
1.6k
views
Generating surrogate variables across multiple variables of interest
sva
18 months ago • updated 17 months ago Robert • 0
0
votes
3
replies
1.8k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 21 months ago by ▴ 870 • written 21 months ago by • 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
21 months ago nhaus ▴ 70
0
votes
2
replies
780
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 months ago michelafrancesconi8 • 0
0
votes
4
replies
1.6k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
21 months ago Lucy ▴ 60
0
votes
8
replies
1.7k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
22 months ago michelafrancesconi8 • 0
0
votes
3
replies
988
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 22 months ago by 68k • written 22 months ago by ▴ 10
0
votes
5
replies
2.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 interaction term + sva
sva DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by ▴ 20
0
votes
2
replies
962
views
combat output NaN
sva
2.2 years ago maxixian1990 • 0
0
votes
4
replies
1.5k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 months ago by 43k • written 2.2 years ago by • 0
5
votes
2
replies
3.0k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
2.3 years ago Federico ▴ 10
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 21 months ago by 53k • written 2.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
votes
3
replies
3.2k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Fluidigm Data Batch Correction
sva limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
3
votes
3
replies
2.7k
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
2.5 years ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.7k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.5 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
0
votes
0
replies
909
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.6 years ago amnahsiddiqa ▴ 10
0
votes
1
reply
1.1k
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
2
votes
2
replies
1.4k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.9 years ago Hatchet • 0
5
votes
2
replies
1.4k
views
Sva and batch effect
limma BatchEffect sva
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3.4 years ago Marie • 0
2
votes
9
replies
2.6k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
vote
0
replies
1.1k
views
Why does surrogate variable confound with variable given in mod?
sva
3.5 years ago shdam ▴ 10
1
vote
3
replies
2.1k
views
Error in shrinkage for DESeq2
sva DESeq2
3.6 years ago Kent • 0
1
vote
1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 20
1
vote
2
replies
2.7k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3.7 years ago • updated 3.6 years ago takemoto • 0
0
votes
1
reply
2.0k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
1
vote
1
reply
2.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 70
1
vote
4
replies
2.7k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.9 years ago Clay • 0
0
votes
0
replies
1.6k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
5
replies
6.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.0 years ago by ★ 5.0k • written 4.8 years ago by • 0
0
votes
0
replies
1.3k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
4.3 years ago georgia.katsoula ▴ 40
1
vote
4
replies
8.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
4.3 years ago NewBioInfo ▴ 10
1
vote
2
replies
2.2k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
4.4 years ago Ahdee ▴ 60
0
votes
1
reply
4.5k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 4.6 years ago by • 0 • written 8.7 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 4.7 years ago by ▴ 60 • written 4.7 years ago by • 0
1
vote
4
replies
3.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 2.2 years ago by • 0 • written 4.9 years ago by • 0
0
votes
1
reply
2.1k
views
How to set mod0 in sva analysis
sva
updated 4.9 years ago by ★ 3.4k • written 4.9 years ago by • 0
2
votes
2
replies
1.6k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
241 results • Page 1 of 5
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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