Showing : SVA • reset
0
votes
2
replies
487
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 10
0
votes
3
replies
461
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 months ago Travis • 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 5 months ago by • 0 • written 7.3 years ago by ▴ 60
0
votes
4
replies
968
views
Generating surrogate variables across multiple variables of interest
sva
6 months ago Robert • 0
0
votes
3
replies
923
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 9 months ago by ▴ 870 • written 9 months ago by • 0
3
votes
6
replies
949
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
9 months ago nhaus ▴ 70
0
votes
2
replies
493
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
9 months ago michelafrancesconi8 • 0
0
votes
4
replies
932
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
9 months ago Lucy ▴ 60
0
votes
8
replies
927
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
10 months ago michelafrancesconi8 • 0
0
votes
3
replies
614
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 10 months ago by 67k • written 10 months ago by ▴ 10
0
votes
5
replies
1.4k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
0
votes
1
reply
740
views
DESeq2 interaction term + sva
sva DESeq2
updated 12 months ago by 43k • written 13 months ago by ▴ 20
0
votes
2
replies
627
views
combat output NaN
sva
14 months ago maxixian1990 • 0
0
votes
4
replies
1.0k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 months ago by 43k • written 15 months ago by • 0
5
votes
2
replies
1.9k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
16 months ago Federico ▴ 10
5
votes
9
replies
2.1k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 9 months ago by 52k • written 16 months ago by ▴ 10
0
votes
1
reply
801
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 17 months ago by 67k • written 17 months ago by • 0
2
votes
3
replies
2.2k
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 17 months ago by 67k • written 17 months ago by ▴ 10
0
votes
2
replies
910
views
Fluidigm Data Batch Correction
sva limma
updated 18 months ago by 52k • written 18 months ago by • 0
3
votes
3
replies
1.8k
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
19 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.0k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 10
0
votes
0
replies
612
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
19 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
812
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
2
votes
2
replies
1.1k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
23 months ago Hatchet • 0
5
votes
2
replies
1.1k
views
Sva and batch effect
limma BatchEffect sva
updated 24 months ago by 52k • written 24 months ago by • 0
0
votes
2
replies
1.1k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.5 years ago Marie • 0
2
votes
9
replies
2.1k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.5 years ago by 67k • written 2.5 years ago by • 0
1
vote
0
replies
849
views
Why does surrogate variable confound with variable given in mod?
sva
2.5 years ago shdam ▴ 10
1
vote
3
replies
1.7k
views
Error in shrinkage for DESeq2
sva DESeq2
2.6 years ago Kent • 0
1
vote
1
reply
945
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.7 years ago by 67k • written 2.7 years ago by ▴ 20
1
vote
2
replies
2.1k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.7 years ago takemoto • 0
0
votes
1
reply
1.4k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
1
vote
1
reply
1.5k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.9 years ago by ★ 4.6k • written 2.9 years ago by ▴ 70
1
vote
4
replies
2.1k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.9 years ago Clay • 0
0
votes
0
replies
1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
0
votes
5
replies
4.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.0 years ago by ★ 4.6k • written 3.8 years ago by • 0
0
votes
0
replies
1.0k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.3 years ago georgia.katsoula ▴ 40
1
vote
4
replies
7.4k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.3 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.7k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.4 years ago Ahdee ▴ 50
0
votes
1
reply
4.0k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.7 years ago by • 0 • written 7.7 years ago by ▴ 10
0
votes
1
reply
2.2k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.7 years ago by ▴ 50 • written 3.7 years ago by • 0
1
vote
4
replies
2.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 15 months ago by • 0 • written 3.9 years ago by • 0
0
votes
1
reply
1.7k
views
How to set mod0 in sva analysis
sva
updated 3.9 years ago by ★ 3.4k • written 3.9 years ago by • 0
2
votes
2
replies
1.3k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.9 years ago by ★ 4.6k • written 3.9 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
4.0 years ago epibio ▴ 10
1
vote
8
replies
1.8k
views
Error in running Combat function
sva ComBat
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 10
0
votes
5
replies
1.4k
views
Variable of interest in combat correction
sva combat
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
10
replies
1.5k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
7
votes
6
replies
2.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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