Showing : SVA • reset
0
votes
2
replies
75
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
7 days ago • updated 4 days ago Marie • 0
2
votes
9
replies
343
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 19 days ago by 60k • written 26 days ago by • 0
1
vote
0
replies
148
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
123
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
238
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
161
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 4 months ago by 46k • written 4 months ago by • 0
1
vote
1
reply
247
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
349
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
290
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
423
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
607
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 15 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
409
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
416
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 22 months ago by 3.6k • written 23 months ago by • 0
0
votes
10
replies
526
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
571
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
304
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
275
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
389
views
SVA paired samples
SVA EPIC methylation limma
updated 2.4 years ago by 60k • written 2.5 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
397
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
917
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
404
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
374
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
566
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
477
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
648
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
495
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
512
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
452
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
444
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
393
views
Design matrix for cohort with samples outside "block"
limma voom sva
3.0 years ago kentfung • 0
0
votes
0
replies
300
views
fsva function does not work without newdat argument
sva
3.0 years ago jakob.wirbel • 0
0
votes
0
replies
376
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
519
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
585
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
824
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
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Comment: errors in annotation by Josie • 0
OK thanks James. I'll send off an email to GenBank, see if they feel inclined to correct some errors.
Answer: Conversion of UniProt to Ensembl by James W. MacDonald 60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles by Fatemeh • 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles by James W. MacDonald 60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws by James W. MacDonald 60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Votes
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
Answer: the difference between getGEO and getGEOSuppFiles
Answer: TPM normalization starting with read counts
Awards • All
Scholar to James W. MacDonald 60k
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