Showing : SVA • reset
0
votes
3
replies
267
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 21 days ago by ▴ 850 • written 28 days ago by • 0
3
votes
6
replies
285
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
29 days ago • updated 28 days ago nhaus ▴ 30
0
votes
2
replies
175
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago michelafrancesconi8 • 0
0
votes
4
replies
440
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
0
votes
8
replies
421
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
314
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 9 weeks ago by 65k • written 10 weeks ago by ▴ 10
0
votes
5
replies
582
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
394
views
DESeq2 interaction term + sva
sva DESeq2
updated 4 months ago by 42k • written 4 months ago by ▴ 20
0
votes
2
replies
345
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
609
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 23 days ago by 42k • written 6 months ago by • 0
5
votes
2
replies
769
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 22 days ago by 50k • written 7 months ago by ▴ 10
0
votes
1
reply
466
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
3
replies
1.1k
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 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
2
replies
631
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 10 months ago by • 0
3
votes
3
replies
947
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
10 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
0
replies
393
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
544
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
2
replies
849
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
15 months ago Hatchet • 0
5
votes
2
replies
776
views
Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
0
votes
2
replies
805
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
21 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 22 months ago by • 0
1
vote
0
replies
681
views
Why does surrogate variable confound with variable given in mod?
sva
22 months ago shdam ▴ 10
1
vote
3
replies
1.4k
views
Error in shrinkage for DESeq2
sva DESeq2
23 months ago Kent • 0
4
votes
3
replies
9.2k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 23 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
1
reply
747
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
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
24 months ago • updated 23 months ago takemoto • 0
0
votes
1
reply
942
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 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 ★ 4.1k • written 2.2 years ago by ▴ 30
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
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
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
0
votes
0
replies
790
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
5.9k
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 3.0 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 3.0 years ago by ▴ 50 • written 3.0 years ago by • 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 3.2 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 ★ 3.3k • written 3.2 years ago by • 0
2
votes
2
replies
990
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
votes
0
replies
972
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 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
1.1k
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 3.7 years ago by 65k • written 3.7 years ago by • 0
7
votes
6
replies
1.7k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.0 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
0
votes
1
reply
772
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 30
0
votes
1
reply
984
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
1
vote
1
reply
951
views
SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
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