Showing : SVA • reset
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
5 weeks ago bbao ▴ 10
0
votes
2
replies
573
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
0
votes
3
replies
660
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
6 months ago Travis • 0
0
votes
4
replies
1.1k
views
Generating surrogate variables across multiple variables of interest
sva
8 months ago Robert • 0
0
votes
3
replies
1.2k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 11 months ago by ▴ 870 • written 11 months ago by • 0
3
votes
6
replies
1.1k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
11 months ago nhaus ▴ 70
0
votes
2
replies
555
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
11 months ago michelafrancesconi8 • 0
0
votes
4
replies
1.1k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
11 months ago Lucy ▴ 60
0
votes
8
replies
1.1k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
12 months ago michelafrancesconi8 • 0
0
votes
3
replies
692
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 12 months ago by 68k • written 13 months ago by ▴ 10
0
votes
5
replies
1.5k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
0
votes
1
reply
806
views
DESeq2 interaction term + sva
sva DESeq2
updated 14 months ago by 43k • written 15 months ago by ▴ 20
0
votes
2
replies
686
views
combat output NaN
sva
16 months ago maxixian1990 • 0
0
votes
4
replies
1.1k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 11 months ago by 43k • written 17 months ago by • 0
5
votes
2
replies
2.1k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
18 months ago Federico ▴ 10
5
votes
9
replies
2.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 11 months ago by 52k • written 18 months ago by ▴ 10
0
votes
1
reply
848
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 19 months ago by 68k • written 19 months ago by • 0
2
votes
3
replies
2.4k
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 19 months ago by 68k • written 19 months ago by ▴ 10
0
votes
2
replies
978
views
Fluidigm Data Batch Correction
sva limma
updated 20 months ago by 52k • written 20 months ago by • 0
3
votes
3
replies
2.1k
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
21 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 21 months ago by ★ 4.8k • written 21 months ago by ▴ 10
0
votes
0
replies
662
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
21 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
867
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by • 0
2
votes
2
replies
1.2k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.1 years ago Hatchet • 0
5
votes
2
replies
1.2k
views
Sva and batch effect
limma BatchEffect sva
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
votes
2
replies
1.1k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.6 years ago Marie • 0
2
votes
9
replies
2.2k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
0
replies
885
views
Why does surrogate variable confound with variable given in mod?
sva
2.7 years ago shdam ▴ 10
1
vote
3
replies
1.8k
views
Error in shrinkage for DESeq2
sva DESeq2
2.8 years ago Kent • 0
1
vote
1
reply
990
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.9 years ago • updated 2.8 years ago takemoto • 0
0
votes
1
reply
1.5k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
1
vote
1
reply
1.7k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.1 years ago by ★ 4.8k • written 3.1 years ago by ▴ 70
1
vote
4
replies
2.2k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.1 years ago Clay • 0
0
votes
0
replies
1.4k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
0
replies
1.1k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.5 years ago georgia.katsoula ▴ 40
1
vote
4
replies
7.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.5 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.8k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.6 years ago Ahdee ▴ 50
0
votes
1
reply
2.4k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.8 years ago by ▴ 60 • written 3.8 years ago by • 0
0
votes
5
replies
5.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.2 years ago by ★ 4.8k • written 4.0 years ago by • 0
1
vote
4
replies
3.1k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 17 months ago by • 0 • written 4.0 years ago by • 0
0
votes
1
reply
1.8k
views
How to set mod0 in sva analysis
sva
updated 4.1 years ago by ★ 3.4k • written 4.1 years ago by • 0
2
votes
2
replies
1.4k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.1 years ago by ★ 4.8k • written 4.1 years ago by • 0
0
votes
0
replies
1.2k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.2 years ago epibio ▴ 10
1
vote
8
replies
1.9k
views
Error in running Combat function
sva ComBat
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Variable of interest in combat correction
sva combat
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
0
votes
10
replies
1.6k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
7
votes
6
replies
2.4k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.9 years ago by ▴ 870 • written 4.9 years ago by ▴ 10
0
votes
1
reply
1.0k
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
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What is the cheapest day to fly on American Airlines? {Ask_Expert}
Answer: Merging annotation with differential expression output
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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