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SVA
•
reset
0
votes
1
reply
131
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 11 weeks ago by
ATpoint
★ 2.8k • written 11 weeks ago by
marslena
• 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
Gordon Smyth
47k • written 3 months ago by
Lenny186
• 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
James W. MacDonald
62k • written 10 months ago by
Jasmin
• 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
wahaha
• 0 • written 5.6 years ago by
anton.kratz
▴ 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
James W. MacDonald
62k • written 12 months ago by
ramonfallon
• 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
Gordon Smyth
47k • written 13 months ago by
Mageiros
• 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
ATpoint
★ 2.8k • written 15 months ago by
nhaus
• 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
James W. MacDonald
62k • written 16 months ago by
Bex
• 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
ATpoint
★ 2.8k • written 2.2 years ago by
Xiaojie Cheng
• 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
vote
4
replies
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
chase.mateusiak
• 0 • written 6.1 years ago by
amoltej
▴ 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
sebastian.lobentanzer
▴ 50 • written 2.0 years ago by
chiwut.wong
• 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
Kevin Blighe
3.8k • written 2.2 years ago by
zeegzaag
• 0
0
votes
1
reply
814
views
How to set mod0 in sva analysis
sva
updated 2.3 years ago by
Robert Castelo
★ 3.0k • written 2.3 years ago by
hank9cao
• 0
2
votes
2
replies
621
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 2.3 years ago by
ATpoint
★ 2.8k • written 2.3 years ago by
MOHAMMAD
• 0
0
votes
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
Kevin Blighe
3.8k • written 2.4 years ago by
Reza
▴ 10
0
votes
5
replies
659
views
Variable of interest in combat correction
sva
combat
updated 2.6 years ago by
James W. MacDonald
62k • written 2.6 years ago by
ch_el
▴ 10
0
votes
3
replies
619
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 2.7 years ago by
Kevin Blighe
3.8k • written 2.7 years ago by
jonellevillar
• 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
James W. MacDonald
62k • written 2.7 years ago by
jonellevillar
• 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
W. Evan Johnson
▴ 840 • written 3.1 years ago by
Zach Roe
▴ 10
0
votes
1
reply
493
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 3.1 years ago by
James W. MacDonald
62k • written 3.1 years ago by
Mozart
▴ 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
James W. MacDonald
62k • written 3.2 years ago by
Nikolay Ivanov
• 0
1
vote
1
reply
594
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 3.2 years ago by
James W. MacDonald
62k • written 3.2 years ago by
whyw6948
• 0
2
votes
4
replies
673
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 3.3 years ago by
Michael Love
40k • written 3.3 years ago by
rihards.saksis
• 0
1
vote
2
replies
585
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 3.4 years ago by
Gordon Smyth
47k • written 3.4 years ago by
vizio12341337
• 0
0
votes
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
W. Evan Johnson
▴ 840 • written 3.5 years ago by
modarzi
▴ 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
James W. MacDonald
62k • written 3.6 years ago by
thkapell
▴ 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
Martin Morgan
25k • written 3.6 years ago by
dhwani2410
• 0
2
votes
5
replies
921
views
SVA for repeated measures design
SVA
deseq2
repeated measures
updated 3.7 years ago by
Robert Castelo
★ 3.0k • written 3.7 years ago by
sara.blocquiaux
• 0
0
votes
1
reply
716
views
Handling adjustment variables and surrogate variables in model
sva
deseq2
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
rbutler
• 0
1
vote
1
reply
768
views
Bioconductor SVA: two variables of interest
sva
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
sara.blocquiaux
• 0
4
votes
5
replies
630
views
Design matrix with intercept for multiple cluster comparison
limma
sva
updated 3.7 years ago by
centralmenu10
• 0 • written 3.8 years ago by
kentfung
▴ 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
Michael Love
40k • written 3.8 years ago by
ege.dedeoglu
• 0
0
votes
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
votes
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
Gordon Smyth
47k • written 3.9 years ago by
Bogdan
▴ 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
keegan
▴ 60 • written 4.0 years ago by
gjl
• 0
50 results • Page
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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…
Votes
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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