Showing : SVA • reset
3
votes
5
replies
1.0k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
15 days ago • updated 14 days ago bbao ▴ 10
0
votes
2
replies
530
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 11 weeks ago by 52k • written 12 weeks ago by ▴ 10
0
votes
3
replies
593
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 months ago Travis • 0
4
votes
5
replies
12k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 6 months ago by • 0 • written 7.4 years ago by ▴ 60
0
votes
4
replies
1.0k
views
Generating surrogate variables across multiple variables of interest
sva
7 months ago Robert • 0
0
votes
3
replies
1.1k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 10 months ago by ▴ 870 • written 10 months ago by • 0
3
votes
6
replies
1.1k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
10 months ago nhaus ▴ 70
0
votes
2
replies
533
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
11 months ago michelafrancesconi8 • 0
0
votes
4
replies
1.0k
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
992
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
11 months ago michelafrancesconi8 • 0
0
votes
3
replies
660
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 12 months ago by 68k • written 12 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 13 months ago by ★ 4.7k • written 14 months ago by • 0
0
votes
1
reply
783
views
DESeq2 interaction term + sva
sva DESeq2
updated 14 months ago by 43k • written 14 months ago by ▴ 20
0
votes
2
replies
662
views
combat output NaN
sva
15 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 10 months ago by 43k • written 16 months ago by • 0
5
votes
2
replies
2.0k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
17 months ago Federico ▴ 10
5
votes
9
replies
2.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 10 months ago by 52k • written 17 months ago by ▴ 10
0
votes
1
reply
826
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 18 months ago by 68k • written 18 months ago by • 0
2
votes
3
replies
2.3k
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 18 months ago by 68k • written 18 months ago by ▴ 10
0
votes
2
replies
956
views
Fluidigm Data Batch Correction
sva limma
updated 19 months ago by 52k • written 19 months ago by • 0
3
votes
3
replies
1.9k
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
20 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 20 months ago by ★ 4.7k • written 20 months ago by ▴ 10
0
votes
0
replies
643
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
20 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
850
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 24 months ago by ★ 4.7k • written 24 months ago by • 0
2
votes
2
replies
1.2k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.0 years ago Hatchet • 0
5
votes
2
replies
1.1k
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
2.1k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
1
vote
0
replies
870
views
Why does surrogate variable confound with variable given in mod?
sva
2.6 years ago shdam ▴ 10
1
vote
3
replies
1.8k
views
Error in shrinkage for DESeq2
sva DESeq2
2.7 years ago Kent • 0
1
vote
1
reply
980
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
2.8 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
1.6k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.0 years ago by ★ 4.7k • written 3.0 years ago by ▴ 70
1
vote
4
replies
2.2k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.0 years ago Clay • 0
0
votes
0
replies
1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
5
replies
5.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.1 years ago by ★ 4.7k • written 3.9 years ago by • 0
0
votes
0
replies
1.0k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.4 years ago georgia.katsoula ▴ 40
1
vote
4
replies
7.7k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.4 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
3.5 years ago Ahdee ▴ 50
0
votes
1
reply
4.1k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.8 years ago by • 0 • written 7.8 years ago by ▴ 10
0
votes
1
reply
2.3k
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
1
vote
4
replies
2.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 16 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 4.0 years ago by ★ 3.4k • written 4.0 years ago by • 0
2
votes
2
replies
1.4k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.0 years ago by ★ 4.7k • written 4.0 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
4.1 years ago epibio ▴ 10
1
vote
8
replies
1.9k
views
Error in running Combat function
sva ComBat
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 10
0
votes
5
replies
1.4k
views
Variable of interest in combat correction
sva combat
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.4 years ago by ★ 4.0k • written 4.4 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
50 results • Page 1 of 1
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Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This post does not fit the theme of this forum.
Comment: Unbalanced experiment with multiple samples from each patient. by canarias • 0
Hi Aaron, I'm faced with an analysis that has basically the same problem as OP had, but is probably even more unbalanced: In most cases, I…
Comment: Gene Set Enrichment Analysis in Bioconductor course by info ▴ 10
If you are interested in Gene Set Enrichment Analysis in R, you can still join us next week for this 4-day Physalia course on GSEA in R and…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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