Showing : SVA • reset
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131
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 11 weeks ago by ★ 2.8k • written 11 weeks ago by • 0
2
votes
2
replies
200
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
3 months ago Hatchet • 0
5
votes
2
replies
285
views
Sva and batch effect
limma BatchEffect sva
updated 3 months ago by 47k • written 3 months ago by • 0
0
votes
2
replies
317
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
9 months ago Marie • 0
2
votes
9
replies
824
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 10 months ago by 62k • written 10 months ago by • 0
1
vote
0
replies
370
views
Why does surrogate variable confound with variable given in mod?
sva
10 months ago shdam ▴ 10
1
vote
3
replies
765
views
Error in shrinkage for DESeq2
sva DESeq2
11 months ago Kent • 0
4
votes
3
replies
7.5k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 12 months ago by • 0 • written 5.6 years ago by ▴ 60
1
vote
1
reply
402
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 12 months ago by 62k • written 12 months ago by • 0
1
vote
2
replies
759
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
12 months ago takemoto • 0
0
votes
1
reply
404
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 13 months ago by 47k • written 13 months ago by • 0
1
vote
1
reply
579
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 15 months ago by ★ 2.8k • written 15 months ago by • 0
1
vote
4
replies
958
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
15 months ago Clay • 0
0
votes
0
replies
662
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 16 months ago by 62k • written 16 months ago by • 0
0
votes
5
replies
2.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 16 months ago by ★ 2.8k • written 2.2 years ago by • 0
0
votes
0
replies
486
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
20 months ago georgia.katsoula ▴ 40
1
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4
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3.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
20 months ago NewBioInfo ▴ 10
1
vote
2
replies
784
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
21 months ago Ahdee ▴ 50
0
votes
1
reply
2.9k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 2.0 years ago by • 0 • written 6.1 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 2.0 years ago by ▴ 50 • written 2.0 years ago by • 0
1
vote
3
replies
924
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
0
votes
1
reply
814
views
How to set mod0 in sva analysis
sva
updated 2.3 years ago by ★ 3.0k • written 2.3 years ago by • 0
2
votes
2
replies
621
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 2.3 years ago by ★ 2.8k • written 2.3 years ago by • 0
0
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0
replies
657
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
2.4 years ago epibio ▴ 10
1
vote
8
replies
980
views
Error in running Combat function
sva ComBat
updated 2.3 years ago by 3.8k • written 2.4 years ago by ▴ 10
0
votes
5
replies
659
views
Variable of interest in combat correction
sva combat
updated 2.6 years ago by 62k • written 2.6 years ago by ▴ 10
0
votes
3
replies
619
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 2.7 years ago by 3.8k • written 2.7 years ago by • 0
0
votes
10
replies
772
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 2.7 years ago by 62k • written 2.7 years ago by • 0
7
votes
6
replies
972
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 3.1 years ago by ▴ 840 • written 3.1 years ago by ▴ 10
0
votes
1
reply
493
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 3.1 years ago by 62k • written 3.1 years ago by ▴ 20
0
votes
1
reply
594
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 3.2 years ago by 62k • written 3.2 years ago by • 0
1
vote
1
reply
594
views
SVA paired samples
SVA EPIC methylation limma
updated 3.2 years ago by 62k • written 3.2 years ago by • 0
2
votes
4
replies
673
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
1
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2
replies
585
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 3.4 years ago by 47k • written 3.4 years ago by • 0
0
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0
replies
1.3k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.4 years ago anne.bozack • 0
0
votes
1
reply
579
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 3.5 years ago by ▴ 840 • written 3.5 years ago by ▴ 10
0
votes
0
replies
563
views
limma-voom group design and its effect on sva
limma voom group-design sva
3.5 years ago kentfung ▴ 10
0
votes
8
replies
851
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 3.6 years ago by 62k • written 3.6 years ago by ▴ 10
0
votes
3
replies
662
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
2
votes
5
replies
921
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 3.7 years ago by ★ 3.0k • written 3.7 years ago by • 0
0
votes
1
reply
716
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 3.7 years ago by 62k • written 3.7 years ago by • 0
1
vote
1
reply
768
views
Bioconductor SVA: two variables of interest
sva
updated 3.7 years ago by 62k • written 3.7 years ago by • 0
4
votes
5
replies
630
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 3.7 years ago by • 0 • written 3.8 years ago by ▴ 10
0
votes
2
replies
766
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
0
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3
replies
569
views
Design matrix for cohort with samples outside "block"
limma voom sva
3.8 years ago kentfung ▴ 10
0
votes
0
replies
448
views
fsva function does not work without newdat argument
sva
3.8 years ago jakob.wirbel • 0
0
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0
replies
531
views
The correct specification of the model matrix to ComBat
ComBat sva
3.8 years ago Sam ▴ 10
7
votes
4
replies
3.1k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 3.9 years ago by 47k • written 3.9 years ago by ▴ 660
0
votes
0
replies
666
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
3.9 years ago kentfung ▴ 10
0
votes
1
reply
856
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 4.0 years ago by ▴ 60 • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
Comment: Submitting BSgenome package for a new assembly by Manish • 0
Thanks for the info. This is very helpful. -Manish
Comment: Merge 2 accounts, or delete 1 account. by shepherl 3.5k
are you talking specifically on the support site or elsewhere also?
Comment: BiocGenerics binary is outdated for macOS ARM by shepherl 3.5k
That is because it is failing from dependencies not being available. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/BiocG…
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flowCore: using read.FCS with which.lines is not time efficient?
Comment: BiocGenerics binary is outdated for macOS ARM
Comment: Submitting BSgenome package for a new assembly
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
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