Showing : SVA • reset
0
votes
3
replies
368
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
8 weeks ago Travis • 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 3 months ago by • 0 • written 7.1 years ago by ▴ 60
0
votes
4
replies
850
views
Generating surrogate variables across multiple variables of interest
sva
4 months ago • updated 3 months ago Robert • 0
0
votes
3
replies
738
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 7 months ago by ▴ 870 • written 7 months ago by • 0
3
votes
6
replies
834
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
7 months ago nhaus ▴ 70
0
votes
2
replies
436
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
7 months ago michelafrancesconi8 • 0
0
votes
4
replies
822
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 months ago Lucy ▴ 60
0
votes
8
replies
828
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 months ago michelafrancesconi8 • 0
0
votes
3
replies
561
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 8 months ago by 67k • written 8 months ago by ▴ 10
0
votes
5
replies
1.2k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 10 months ago by ★ 4.5k • written 10 months ago by • 0
0
votes
1
reply
667
views
DESeq2 interaction term + sva
sva DESeq2
updated 10 months ago by 42k • written 11 months ago by ▴ 20
0
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2
replies
574
views
combat output NaN
sva
12 months ago maxixian1990 • 0
0
votes
4
replies
949
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 months ago by 42k • written 13 months ago by • 0
5
votes
2
replies
1.7k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
14 months ago Federico ▴ 10
5
votes
9
replies
1.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 7 months ago by 51k • written 14 months ago by ▴ 10
0
votes
1
reply
745
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 15 months ago by 67k • written 15 months ago by • 0
2
votes
3
replies
1.9k
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 15 months ago by 67k • written 15 months ago by ▴ 10
0
votes
2
replies
868
views
Fluidigm Data Batch Correction
sva limma
updated 16 months ago by 51k • written 16 months ago by • 0
3
votes
3
replies
1.6k
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
17 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 17 months ago by ★ 4.5k • written 17 months ago by ▴ 10
0
votes
0
replies
564
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
17 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
773
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 20 months ago by ★ 4.5k • written 20 months ago by • 0
2
votes
2
replies
1.1k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
21 months ago Hatchet • 0
5
votes
2
replies
1.0k
views
Sva and batch effect
limma BatchEffect sva
updated 22 months ago by 51k • written 22 months ago by • 0
0
votes
2
replies
1.0k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.3 years ago Marie • 0
2
votes
9
replies
2.0k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
1
vote
0
replies
816
views
Why does surrogate variable confound with variable given in mod?
sva
2.4 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
909
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 20
1
vote
2
replies
2.0k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.5 years ago takemoto • 0
0
votes
1
reply
1.3k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.6 years ago by 51k • written 2.6 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 2.8 years ago by ★ 4.5k • written 2.8 years ago by ▴ 70
1
vote
4
replies
2.0k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
2.8 years ago • updated 2.7 years ago Clay • 0
0
votes
0
replies
1.3k
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
4.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.5k • written 3.7 years ago by • 0
0
votes
0
replies
952
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.2 years ago • updated 3.1 years ago georgia.katsoula ▴ 40
1
vote
4
replies
7.1k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.2 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
3.3 years ago Ahdee ▴ 50
0
votes
1
reply
3.9k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3.5 years ago by • 0 • written 7.6 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.5 years ago by ▴ 50 • written 3.5 years ago by • 0
1
vote
4
replies
2.7k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 13 months ago by • 0 • written 3.7 years ago by • 0
0
votes
1
reply
1.7k
views
How to set mod0 in sva analysis
sva
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
2
votes
2
replies
1.3k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.8 years ago by ★ 4.5k • written 3.8 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 3.9 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Variable of interest in combat correction
sva combat
updated 4.1 years ago by 67k • written 4.1 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 4.2 years ago by • 0
0
votes
10
replies
1.4k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.2 years ago by 67k • written 4.2 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 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
0
votes
1
reply
942
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.6 years ago by 67k • written 4.6 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
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