Showing : sva • reset
0
votes
3
replies
224
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 7 days ago by ▴ 850 • written 13 days ago by • 0
3
votes
6
replies
234
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
14 days ago nhaus ▴ 30
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago • updated 22 days ago michelafrancesconi8 • 0
0
votes
4
replies
392
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
24 days ago • updated 23 days ago Lucy ▴ 60
0
votes
8
replies
377
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
291
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 7 weeks ago by 65k • written 7 weeks ago by ▴ 10
0
votes
5
replies
521
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
381
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
330
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
572
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 days ago by 41k • written 6 months ago by • 0
5
votes
2
replies
725
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
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 days ago by 50k • written 7 months ago by ▴ 10
0
votes
1
reply
444
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
606
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
912
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
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
0
votes
0
replies
382
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
531
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
820
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
5
votes
2
replies
759
views
Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
0
votes
2
replies
780
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
674
views
Why does surrogate variable confound with variable given in mod?
sva
21 months ago shdam ▴ 10
1
vote
3
replies
1.4k
views
Error in shrinkage for DESeq2
sva DESeq2
22 months ago Kent • 0
1
vote
1
reply
739
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
23 months ago takemoto • 0
0
votes
1
reply
914
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
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
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
0
replies
780
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
5.8k
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
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
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
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
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
973
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
0
votes
0
replies
959
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 3.2 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
1.0k
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
7
votes
6
replies
1.6k
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
759
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
0
votes
1
reply
965
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
1
vote
1
reply
940
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
2
votes
4
replies
1.0k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
1
vote
2
replies
924
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 4.3 years ago by 50k • written 4.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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