Showing : SVA • reset
0
votes
2
replies
52
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3 days ago • updated 4 hours ago Marie • 0
2
votes
9
replies
336
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 15 days ago by 60k • written 22 days ago by • 0
1
vote
0
replies
142
views
Why does surrogate variable confound with variable given in mod?
sva
29 days ago shdam ▴ 10
1
vote
3
replies
336
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 10 weeks ago by • 0 • written 4.8 years ago by ▴ 60
1
vote
2
replies
231
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
12 weeks ago • updated 11 weeks ago takemoto • 0
1
vote
1
reply
120
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
0
votes
1
reply
160
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3 months ago by 46k • written 3 months ago by • 0
4
votes
3
replies
1.5k
views
Blocked design and Surrogate Variables Analsysis(SVA)
limma sva block
updated 5 months ago by • 0 • written 7.8 years ago by ▴ 20
1
vote
4
replies
441
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
5 months ago Clay • 0
1
vote
1
reply
241
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
0
votes
0
replies
341
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 6 months ago by ★ 1.4k • written 16 months ago by • 0
0
votes
0
replies
287
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
419
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
601
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 14 months ago by ▴ 50 • written 14 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
407
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
1
vote
8
replies
624
views
Error in running Combat function
sva ComBat
updated 18 months ago by 3.6k • written 19 months ago by ▴ 10
0
votes
0
replies
471
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
18 months ago epibio ▴ 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
522
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
567
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
301
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
273
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
386
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
457
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
392
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
911
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
401
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
370
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
562
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
473
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
643
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
505
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
449
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 2.9 years ago by • 0 • written 3.0 years ago by • 0
0
votes
2
replies
442
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
373
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
578
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
819
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
50 results • Page 1 of 1
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Comment: DESeq2 LFC changes sign after adjusting for surrogates by Marie • 0
Thanks a lot!
Comment: how to use Rsamtools to parse extra fields from STAR alignment by Jiping Wang ▴ 90
Thanks so much! That's exactly the solution I am looking for.
Comment: Mapping genome regions to gene symbols by michaelwegert • 0
function > elementLengths() was deprecated in S4Vectors version update 0.16.0 (in 2016?). \ So I used: > elementNROWS() [https://web.m…
Comment: OPLS-DA: confidence interval for accuracy metric by etienne.thevenot ▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package by xlal • 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Votes
Answer: error running UniProt.ws
error running UniProt.ws
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
how to use Rsamtools to parse extra fields from STAR alignment
Comment: how to use Rsamtools to parse extra fields from STAR alignment
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