Showing : sva • reset
0
votes
3
replies
320
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
29 days ago • updated 28 days ago Travis • 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 9 weeks ago by • 0 • written 7.0 years ago by ▴ 60
0
votes
4
replies
798
views
Generating surrogate variables across multiple variables of interest
sva
3 months ago Robert • 0
0
votes
3
replies
635
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 6 months ago by ▴ 860 • written 6 months ago by • 0
3
votes
6
replies
760
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
6 months ago nhaus ▴ 70
0
votes
2
replies
410
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
6 months ago michelafrancesconi8 • 0
0
votes
4
replies
772
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 months ago Lucy ▴ 60
0
votes
8
replies
793
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 months ago michelafrancesconi8 • 0
0
votes
3
replies
536
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 7 months ago by 67k • written 7 months ago by ▴ 10
0
votes
5
replies
1.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
0
votes
1
reply
634
views
DESeq2 interaction term + sva
sva DESeq2
updated 9 months ago by 42k • written 10 months ago by ▴ 20
0
votes
2
replies
548
views
combat output NaN
sva
11 months ago maxixian1990 • 0
0
votes
4
replies
898
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 6 months ago by 42k • written 12 months ago by • 0
5
votes
2
replies
1.5k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
13 months ago Federico ▴ 10
5
votes
9
replies
1.8k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 6 months ago by 51k • written 13 months ago by ▴ 10
0
votes
1
reply
723
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 14 months ago by 67k • written 14 months ago by • 0
2
votes
3
replies
1.8k
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 14 months ago by 67k • written 14 months ago by ▴ 10
0
votes
2
replies
843
views
Fluidigm Data Batch Correction
sva limma
updated 15 months ago by 51k • written 15 months ago by • 0
3
votes
3
replies
1.5k
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
16 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.8k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 16 months ago by ★ 4.5k • written 16 months ago by ▴ 10
0
votes
0
replies
540
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
16 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
751
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 19 months ago by ★ 4.5k • written 19 months ago by • 0
2
votes
2
replies
1.1k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
20 months ago Hatchet • 0
5
votes
2
replies
1.0k
views
Sva and batch effect
limma BatchEffect sva
updated 21 months ago by 51k • written 21 months ago by • 0
0
votes
2
replies
1.0k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.2 years ago Marie • 0
2
votes
9
replies
2.0k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.2 years ago by 67k • written 2.3 years ago by • 0
1
vote
0
replies
800
views
Why does surrogate variable confound with variable given in mod?
sva
2.3 years ago shdam ▴ 10
1
vote
3
replies
1.6k
views
Error in shrinkage for DESeq2
sva DESeq2
2.4 years ago Kent • 0
1
vote
1
reply
890
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 20
1
vote
2
replies
2.0k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.4 years ago takemoto • 0
0
votes
1
reply
1.2k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.5 years ago by 51k • written 2.5 years ago by • 0
1
vote
1
reply
1.4k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.7 years ago by ★ 4.5k • written 2.7 years ago by ▴ 70
1
vote
4
replies
2.0k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.7 years ago Clay • 0
0
votes
0
replies
1.2k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
0
votes
5
replies
4.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.8 years ago by ★ 4.5k • written 3.6 years ago by • 0
0
votes
0
replies
932
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.1 years ago georgia.katsoula ▴ 40
1
vote
4
replies
6.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.1 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.6k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.2 years ago Ahdee ▴ 50
0
votes
1
reply
3.8k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.4 years ago by • 0 • written 7.5 years ago by ▴ 10
0
votes
1
reply
2.0k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.4 years ago by ▴ 50 • written 3.4 years ago by • 0
1
vote
4
replies
2.6k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 12 months ago by • 0 • written 3.6 years ago by • 0
0
votes
1
reply
1.6k
views
How to set mod0 in sva analysis
sva
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
2
votes
2
replies
1.2k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.7 years ago by ★ 4.5k • written 3.7 years ago by • 0
0
votes
0
replies
1.1k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.8 years ago epibio ▴ 10
1
vote
8
replies
1.7k
views
Error in running Combat function
sva ComBat
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Variable of interest in combat correction
sva combat
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
votes
10
replies
1.4k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
7
votes
6
replies
2.1k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.5 years ago by ▴ 860 • written 4.5 years ago by ▴ 10
0
votes
1
reply
926
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Analysis of 2*4 factorial design by Gordon Smyth 51k
This is covered by Section 9.5 of the limma User's Guide. The analysis with a single-factor is much better. Your definition of A2 vs A1 …
Comment: Zero intra-block correlation in RRBS analysis using voomLmFit with block by Gordon Smyth 51k
It might be ok to estimate the intrablock correlation from the M-values. But then, if you do that, you may as well do the whole analysis in…
Answer: limma technical repeat correction by Gordon Smyth 51k
The technical samples should be averaged. Then use duplicateCorrelation() with block=PatientID.
Comment: New to mass spec data analysis by abhisek001 • 0
Thanks for your kind responses.
Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP by Anni • 0
I encountered the same problem. Problem seems to be "make_se()" function that does *not* use variable 'label' to bind colData to assay, but…
Votes
Differential expression analysis starting from TPM data
Answer: How to identify top most variable genes from log2 normalized data?
Answer: How to identify top most variable genes from log2 normalized data?
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Awards • All
Popular Question to Bioinformagician • 0
Teacher to Gordon Smyth 51k
Scholar to James W. MacDonald 67k
Teacher to Peter Langfelder ★ 3.0k
Popular Question to Assa Yeroslaviz ★ 1.5k
Locations • All
France, 8 minutes ago
United States, 12 minutes ago
United States, 15 minutes ago
India, 44 minutes ago
Ireland, 44 minutes ago
Traffic: 496 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6