Showing : SVA • reset
0
votes
0
replies
202
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
3 months ago dudwnsrla1 • 0
0
votes
1
reply
600
views
Combat-seq usage
sva
3 months ago bbao ▴ 10
0
votes
0
replies
278
views
Batch correction for microarray
BatchEffect sva MicroarrayData
4 months ago Shaimaa Gamal • 0
1
vote
1
reply
945
views
ComBat with repeated measures
ComBat sva
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
3
votes
5
replies
1.4k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
6 months ago bbao ▴ 10
0
votes
2
replies
795
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 9 months ago by 52k • written 9 months ago by ▴ 10
0
votes
3
replies
970
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
11 months ago Travis • 0
4
votes
5
replies
12k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 12 months ago by • 0 • written 7.9 years ago by ▴ 60
0
votes
4
replies
1.3k
views
Generating surrogate variables across multiple variables of interest
sva
13 months ago Robert • 0
0
votes
3
replies
1.5k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 16 months ago by ▴ 870 • written 16 months ago by • 0
3
votes
6
replies
1.4k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
17 months ago • updated 16 months ago nhaus ▴ 70
0
votes
2
replies
656
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 months ago michelafrancesconi8 • 0
0
votes
4
replies
1.3k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
17 months ago Lucy ▴ 60
0
votes
8
replies
1.3k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
18 months ago michelafrancesconi8 • 0
0
votes
3
replies
804
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 18 months ago by 68k • written 18 months ago by ▴ 10
0
votes
5
replies
1.8k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 20 months ago by ★ 4.9k • written 20 months ago by • 0
0
votes
1
reply
927
views
DESeq2 interaction term + sva
sva DESeq2
updated 20 months ago by 43k • written 20 months ago by ▴ 20
0
votes
2
replies
826
views
combat output NaN
sva
22 months ago • updated 21 months ago maxixian1990 • 0
0
votes
4
replies
1.3k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 months ago by 43k • written 22 months ago by • 0
5
votes
2
replies
2.6k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
23 months ago Federico ▴ 10
5
votes
9
replies
2.6k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 16 months ago by 52k • written 23 months ago by ▴ 10
0
votes
1
reply
958
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
2
votes
3
replies
2.9k
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 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Fluidigm Data Batch Correction
sva limma
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
3
votes
3
replies
2.4k
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
2.2 years ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.4k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by ▴ 10
0
votes
0
replies
814
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.2 years ago amnahsiddiqa ▴ 10
0
votes
1
reply
988
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by • 0
2
votes
2
replies
1.3k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.6 years ago Hatchet • 0
5
votes
2
replies
1.3k
views
Sva and batch effect
limma BatchEffect sva
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3.1 years ago Marie • 0
2
votes
9
replies
2.4k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
0
replies
970
views
Why does surrogate variable confound with variable given in mod?
sva
3.1 years ago shdam ▴ 10
1
vote
3
replies
1.9k
views
Error in shrinkage for DESeq2
sva DESeq2
3.2 years ago Kent • 0
1
vote
1
reply
1.1k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 20
1
vote
2
replies
2.5k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3.3 years ago takemoto • 0
0
votes
1
reply
1.8k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.4 years ago by 52k • written 3.4 years ago by • 0
1
vote
1
reply
2.0k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.5 years ago by ★ 4.9k • written 3.5 years ago by ▴ 70
1
vote
4
replies
2.5k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.5 years ago Clay • 0
0
votes
0
replies
1.5k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
5
replies
5.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.6 years ago by ★ 4.9k • written 4.4 years ago by • 0
0
votes
0
replies
1.2k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.9 years ago georgia.katsoula ▴ 40
1
vote
4
replies
8.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
4.0 years ago NewBioInfo ▴ 10
1
vote
2
replies
2.0k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
4.1 years ago Ahdee ▴ 60
0
votes
1
reply
4.3k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 4.3 years ago by • 0 • written 8.4 years ago by ▴ 10
0
votes
1
reply
2.6k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 4.3 years ago by ▴ 60 • written 4.3 years ago by • 0
1
vote
4
replies
3.5k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 22 months ago by • 0 • written 4.5 years ago by • 0
0
votes
1
reply
2.0k
views
How to set mod0 in sva analysis
sva
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by • 0
2
votes
2
replies
1.5k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.5 years ago by ★ 4.9k • written 4.6 years ago by • 0
0
votes
0
replies
1.3k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.6 years ago epibio ▴ 10
240 results • Page 1 of 5
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Comment: Biological Pathway Database by peterparkerrbu • 0
Having the pathways available in PowerPoint format is a huge plus, as it makes them easy to use for presentations and teaching. The ability…
Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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