Showing : SVA • reset
0
votes
3
replies
201
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 1 day ago by ▴ 850 • written 8 days ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 2 days ago by 50k • written 6 months ago by ▴ 10
0
votes
4
replies
557
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 3 days ago by 41k • written 5 months ago by • 0
3
votes
6
replies
217
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
9 days ago • updated 8 days ago nhaus ▴ 30
0
votes
2
replies
145
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 days ago michelafrancesconi8 • 0
0
votes
4
replies
387
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 days ago • updated 17 days ago Lucy ▴ 60
0
votes
8
replies
369
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
278
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 7 weeks ago by ▴ 10
0
votes
5
replies
497
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
370
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
325
views
combat output NaN
sva
5 months ago maxixian1990 • 0
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
5
votes
2
replies
698
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
6 months ago Federico ▴ 10
0
votes
1
reply
432
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 7 months ago by 65k • written 8 months ago by • 0
2
votes
3
replies
1.0k
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
598
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
895
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
9 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
votes
0
replies
378
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
9 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
525
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
votes
2
replies
810
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
5
votes
2
replies
751
views
Sva and batch effect
limma BatchEffect sva
updated 14 months ago by 50k • written 14 months ago by • 0
4
votes
3
replies
5.2k
views
svaseq: how many and which surrogate variables to pick
sva
updated 16 months ago by • 0 • written 8.7 years ago by ▴ 10
2
votes
17
replies
2.3k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 17 months ago by 41k • written 5.1 years ago by • 0
4
votes
8
replies
5.7k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 20 months ago by • 0 • written 6.0 years ago by ▴ 70
0
votes
2
replies
775
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
20 months ago Marie • 0
2
votes
9
replies
1.6k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 21 months ago by 65k • written 21 months ago by • 0
1
vote
0
replies
670
views
Why does surrogate variable confound with variable given in mod?
sva
21 months ago shdam ▴ 10
1
vote
3
replies
1.3k
views
Error in shrinkage for DESeq2
sva DESeq2
22 months ago Kent • 0
4
votes
3
replies
9.1k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 23 months ago by • 0 • written 6.5 years ago by ▴ 60
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
1
vote
1
reply
735
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 23 months ago by 65k • written 23 months ago by ▴ 20
0
votes
1
reply
903
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
4
votes
3
replies
2.0k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma sva block
updated 2.1 years ago by • 0 • written 9.5 years ago by ▴ 20
1
vote
4
replies
1.7k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.2 years ago Clay • 0
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by ▴ 30
0
votes
0
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
0
replies
775
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
2.6 years ago georgia.katsoula ▴ 40
1
vote
4
replies
5.7k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.6 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.4k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
2.7 years ago Ahdee ▴ 50
0
votes
1
reply
3.4k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 2.9 years ago by • 0 • written 7.0 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 2.9 years ago by ▴ 50 • written 2.9 years ago by • 0
0
votes
1
reply
1.3k
views
How to set mod0 in sva analysis
sva
updated 3.2 years ago by ★ 3.2k • written 3.2 years ago by • 0
2
votes
2
replies
968
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.2 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
0
votes
0
replies
952
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.2 years ago epibio ▴ 10
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva combat
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
0
votes
3
replies
1.0k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
10
replies
1.2k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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