Showing : sva • reset
0
votes
2
replies
66
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
5 days ago • updated 2 days ago Marie • 0
2
votes
9
replies
341
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 17 days ago by 60k • written 24 days ago by • 0
1
vote
0
replies
147
views
Why does surrogate variable confound with variable given in mod?
sva
4 weeks ago shdam ▴ 10
1
vote
3
replies
341
views
Error in shrinkage for DESeq2
sva DESeq2
8 weeks ago Kent • 0
4
votes
3
replies
5.7k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 11 weeks ago by • 0 • written 4.8 years ago by ▴ 60
1
vote
1
reply
121
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 11 weeks ago by 60k • written 11 weeks ago by • 0
1
vote
2
replies
234
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
12 weeks ago • updated 11 weeks ago takemoto • 0
0
votes
1
reply
160
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3 months ago by 46k • written 4 months ago by • 0
1
vote
1
reply
245
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
4
replies
442
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
5 months ago Clay • 0
0
votes
0
replies
346
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 6 months ago by 60k • written 6 months ago by • 0
0
votes
5
replies
1.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 7 months ago by ★ 1.4k • written 16 months ago by • 0
0
votes
0
replies
289
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
10 months ago georgia.katsoula ▴ 40
1
vote
4
replies
1.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
10 months ago NewBioInfo ▴ 10
1
vote
2
replies
421
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
12 months ago Ahdee ▴ 50
0
votes
1
reply
2.5k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 14 months ago by • 0 • written 5.3 years ago by ▴ 10
0
votes
1
reply
604
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 14 months ago by ▴ 50 • written 15 months ago by • 0
1
vote
3
replies
500
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 17 months ago by 3.6k • written 17 months ago by • 0
0
votes
1
reply
495
views
How to set mod0 in sva analysis
sva
updated 18 months ago by ★ 2.9k • written 18 months ago by • 0
2
votes
2
replies
408
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
0
votes
0
replies
471
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
19 months ago epibio ▴ 10
1
vote
8
replies
625
views
Error in running Combat function
sva ComBat
updated 18 months ago by 3.6k • written 19 months ago by ▴ 10
0
votes
5
replies
443
views
Variable of interest in combat correction
sva combat
updated 21 months ago by 60k • written 21 months ago by ▴ 10
0
votes
3
replies
414
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 22 months ago by 3.6k • written 22 months ago by • 0
0
votes
10
replies
523
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 23 months ago by 60k • written 23 months ago by • 0
7
votes
6
replies
568
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 2.3 years ago by ▴ 840 • written 2.3 years ago by ▴ 10
0
votes
1
reply
302
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 2.3 years ago by 60k • written 2.3 years ago by ▴ 20
0
votes
1
reply
274
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 2.4 years ago by 60k • written 2.4 years ago by • 0
1
vote
1
reply
388
views
SVA paired samples
SVA EPIC methylation limma
updated 2.4 years ago by 60k • written 2.4 years ago by • 0
2
votes
4
replies
458
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 2.5 years ago by 37k • written 2.5 years ago by • 0
1
vote
2
replies
394
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 2.6 years ago by 46k • written 2.6 years ago by • 0
0
votes
0
replies
916
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
2.6 years ago anne.bozack • 0
0
votes
1
reply
403
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 2.7 years ago by ▴ 840 • written 2.7 years ago by ▴ 10
0
votes
0
replies
373
views
limma-voom group design and its effect on sva
limma voom group-design sva
2.7 years ago kentfung • 0
0
votes
8
replies
563
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 2.8 years ago by 60k • written 2.8 years ago by ▴ 10
0
votes
3
replies
476
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
2
votes
5
replies
647
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 2.9 years ago by ★ 2.9k • written 2.9 years ago by • 0
0
votes
1
reply
493
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 2.9 years ago by 60k • written 2.9 years ago by • 0
1
vote
1
reply
508
views
Bioconductor SVA: two variables of interest
sva
updated 2.9 years ago by 60k • written 2.9 years ago by • 0
4
votes
5
replies
450
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 3.0 years ago by • 0 • written 3.0 years ago by • 0
0
votes
2
replies
443
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 3.0 years ago by 37k • written 3.0 years ago by • 0
0
votes
3
replies
392
views
Design matrix for cohort with samples outside "block"
limma voom sva
3.0 years ago kentfung • 0
0
votes
0
replies
299
views
fsva function does not work without newdat argument
sva
3.0 years ago jakob.wirbel • 0
0
votes
0
replies
375
views
The correct specification of the model matrix to ComBat
ComBat sva
3.0 years ago Sam ▴ 10
7
votes
4
replies
2.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 3.1 years ago by 46k • written 3.1 years ago by ▴ 640
0
votes
0
replies
518
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
3.1 years ago kentfung • 0
0
votes
1
reply
581
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 3.2 years ago by ▴ 60 • written 3.2 years ago by • 0
2
votes
8
replies
1.4k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 3.2 years ago by 37k • written 3.2 years ago by ▴ 10
2
votes
1
reply
821
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
3.2 years ago epibio ▴ 10
5
votes
3
replies
1.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 3.2 years ago by ★ 2.7k • written 3.2 years ago by ▴ 260
50 results • Page 1 of 1
Recent ...
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Comment: IsoformSwitchAnalyzeR package on mouse data by bpshtiwan ▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Comment: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws by James W. MacDonald 60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks by Tiago C. Silva ▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks by Marcel Ramos 570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
Awards • All
Centurion to Marcel Ramos 570
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