Showing : SVA • reset
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11
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Batch correction for microarray
BatchEffect sva MicroarrayData
4 hours ago Shaimaa Gamal • 0
1
vote
1
reply
767
views
ComBat with repeated measures
ComBat sva
updated 23 days ago by ★ 4.8k • written 24 days ago by • 0
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
9 weeks ago bbao ▴ 10
0
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2
replies
610
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
0
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3
replies
727
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
6 months ago Travis • 0
0
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4
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1.2k
views
Generating surrogate variables across multiple variables of interest
sva
9 months ago • updated 8 months ago Robert • 0
0
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3
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1.3k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 12 months ago by ▴ 870 • written 12 months ago by • 0
3
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6
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1.2k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 months ago nhaus ▴ 70
0
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2
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577
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
12 months ago michelafrancesconi8 • 0
0
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4
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1.1k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
12 months ago Lucy ▴ 60
0
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8
replies
1.1k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
13 months ago michelafrancesconi8 • 0
0
votes
3
replies
713
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 13 months ago by 68k • written 13 months ago by ▴ 10
0
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5
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1.6k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
0
votes
1
reply
829
views
DESeq2 interaction term + sva
sva DESeq2
updated 15 months ago by 43k • written 16 months ago by ▴ 20
0
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2
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705
views
combat output NaN
sva
17 months ago maxixian1990 • 0
0
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4
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1.2k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 12 months ago by 43k • written 18 months ago by • 0
5
votes
2
replies
2.3k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
19 months ago Federico ▴ 10
5
votes
9
replies
2.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 12 months ago by 52k • written 19 months ago by ▴ 10
0
votes
1
reply
866
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 20 months ago by 68k • written 20 months ago by • 0
2
votes
3
replies
2.6k
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 20 months ago by 68k • written 20 months ago by ▴ 10
0
votes
2
replies
990
views
Fluidigm Data Batch Correction
sva limma
updated 21 months ago by 52k • written 21 months ago by • 0
3
votes
3
replies
2.2k
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
22 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
2.3k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 22 months ago by ★ 4.8k • written 22 months ago by ▴ 10
0
votes
0
replies
679
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
22 months ago amnahsiddiqa ▴ 10
0
votes
1
reply
887
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by • 0
2
votes
2
replies
1.2k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.2 years ago Hatchet • 0
5
votes
2
replies
1.2k
views
Sva and batch effect
limma BatchEffect sva
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
votes
2
replies
1.2k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
2.7 years ago Marie • 0
2
votes
9
replies
2.3k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.7 years ago by 68k • written 2.8 years ago by • 0
1
vote
0
replies
896
views
Why does surrogate variable confound with variable given in mod?
sva
2.8 years ago shdam ▴ 10
1
vote
3
replies
1.8k
views
Error in shrinkage for DESeq2
sva DESeq2
2.8 years ago Kent • 0
1
vote
1
reply
1.0k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 20
1
vote
2
replies
2.3k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.9 years ago takemoto • 0
0
votes
1
reply
1.6k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.0 years ago by 52k • written 3.0 years ago by • 0
1
vote
1
reply
1.7k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.2 years ago by ★ 4.8k • written 3.2 years ago by ▴ 70
1
vote
4
replies
2.3k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.2 years ago Clay • 0
0
votes
0
replies
1.4k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
0
replies
1.1k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.6 years ago georgia.katsoula ▴ 40
1
vote
4
replies
8.0k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.6 years ago NewBioInfo ▴ 10
1
vote
2
replies
1.9k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.7 years ago Ahdee ▴ 60
0
votes
1
reply
2.4k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3.9 years ago by ▴ 60 • written 3.9 years ago by • 0
0
votes
5
replies
5.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
1
vote
4
replies
3.2k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 18 months ago by • 0 • written 4.1 years ago by • 0
0
votes
1
reply
1.9k
views
How to set mod0 in sva analysis
sva
updated 4.2 years ago by ★ 3.4k • written 4.2 years ago by • 0
2
votes
2
replies
1.4k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.2 years ago by ★ 4.8k • written 4.2 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
4.3 years ago epibio ▴ 10
1
vote
8
replies
2.0k
views
Error in running Combat function
sva ComBat
updated 4.2 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Variable of interest in combat correction
sva combat
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
votes
10
replies
1.6k
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
50 results • Page 1 of 1
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Comment: DeSeq Strategies for run to run Replication by Michael Love 43k
You shouldn't need to run `DESeq` on the test data, or manually compute normalization factors. ``` dds_test <- ... # create object dds_te…
Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k
We have made significant changes to how featureCounts annotates junctions detected in read mapping results. These updates are included in t…
Comment: How to perform batch correction on scRNA-seq with confounding plate effects? by 瑞宏 • 0
I would like to share my own understanding: in single-cell RNA sequencing (scRNA-seq), batch correction is solely intended to identify the …
Comment: DiffBind can't find a DAR by Mengjun • 0
Additionally, i checked my bigwig in igv, it shows that the ctrl_1 is more like ko_1, and ctrl_2's track is more like ko_2's track. Did an…
Comment: European Bioconductor Conference 2023 planning by ht • 0
Great news about the European Bioconductor Conference 2023 planning! As someone who enjoys statistical computing and bioinformatics, I'm ex…
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Comment: Differential expression analysis using two TCGA datasets
C: Annotating HTA 2.0 genes
C: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
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