Showing : SVA • reset
0
votes
0
replies
1.4k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
5.0 years ago epibio ▴ 10
1
vote
8
replies
2.3k
views
Error in running Combat function
sva ComBat
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 10
0
votes
5
replies
1.9k
views
Variable of interest in combat correction
sva combat
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
0
votes
10
replies
2.0k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
7
votes
6
replies
3.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 5.7 years ago by ▴ 870 • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.2k
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 30
0
votes
1
reply
1.4k
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
1
reply
1.5k
views
SVA paired samples
SVA EPIC methylation limma
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
2
votes
4
replies
1.7k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
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2
replies
1.5k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
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0
replies
3.0k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
6.0 years ago anne.bozack • 0
0
votes
1
reply
1.4k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 6.1 years ago by ▴ 870 • written 6.1 years ago by ▴ 10
0
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0
replies
1.2k
views
limma-voom group design and its effect on sva
limma voom group-design sva
6.1 years ago kentfung ▴ 20
0
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8
replies
2.2k
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 10
0
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3
replies
1.5k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
2
votes
5
replies
2.3k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 6.3 years ago by ★ 3.4k • written 6.3 years ago by • 0
0
votes
1
reply
1.6k
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
1
reply
1.8k
views
Bioconductor SVA: two variables of interest
sva
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
4
votes
5
replies
1.5k
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 6.4 years ago by • 0 • written 6.4 years ago by ▴ 20
0
votes
2
replies
1.8k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
3
replies
1.4k
views
Design matrix for cohort with samples outside "block"
limma voom sva
6.4 years ago kentfung ▴ 20
0
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0
replies
833
views
fsva function does not work without newdat argument
sva
6.4 years ago jakob.wirbel • 0
0
votes
0
replies
1.2k
views
The correct specification of the model matrix to ComBat
ComBat sva
6.4 years ago Sam ▴ 10
8
votes
4
replies
5.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 670
0
votes
0
replies
1.4k
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.5 years ago kentfung ▴ 20
1
vote
1
reply
2.2k
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 6.6 years ago by ▴ 60 • written 6.6 years ago by ▴ 10
2
votes
8
replies
4.4k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
2
votes
1
reply
2.2k
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
6.6 years ago epibio ▴ 10
5
votes
3
replies
3.3k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by ▴ 280
0
votes
1
reply
1.2k
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 30
3
votes
12
replies
5.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 10
1
vote
1
reply
1.4k
views
svaseq - over adjustment
svaseq sva
6.8 years ago flippy23 • 0
2
votes
17
replies
3.9k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 3.2 years ago by 43k • written 6.8 years ago by • 0
1
vote
2
replies
2.1k
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by ▴ 30
4
votes
4
replies
3.2k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 680
0
votes
0
replies
1.7k
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
1
vote
1
reply
1.2k
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 7.0 years ago by ▴ 570 • written 7.0 years ago by • 0
1
vote
7
replies
2.0k
views
paired sample - SVA model matrix
limma sva paired sample
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
1
vote
1
reply
1.5k
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
7.2 years ago Sebastian Hesse ▴ 70
1
vote
10
replies
8.4k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
votes
0
replies
768
views
Sva for tumor cellular heterogeneity
limma sva
7.3 years ago chp950 • 0
0
votes
2
replies
2.1k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
0
replies
1.4k
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
7.4 years ago jmsendoya • 0
0
votes
1
reply
2.7k
views
A problem in using Combat
sva combat
updated 7.6 years ago by ▴ 870 • written 7.6 years ago by • 0
3
votes
4
replies
2.2k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 20
1
vote
6
replies
1.9k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
7.7 years ago aec ▴ 90
4
votes
8
replies
8.1k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 3.4 years ago by • 0 • written 7.8 years ago by ▴ 70
3
votes
7
replies
6.6k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.8 years ago by ▴ 30 • written 9.9 years ago by ▴ 40
8
votes
3
replies
6.0k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
8.0 years ago kevin.kingsland ▴ 70
241 results • Page 2 of 5
Recent ...
Replies
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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