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sva
•
reset
0
votes
8
replies
253
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
11 days ago
michelafrancesconi8
• 0
0
votes
3
replies
204
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 14 days ago by
James W. MacDonald
65k • written 18 days ago by
MEME
▴ 10
0
votes
5
replies
428
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 10 weeks ago by
ATpoint
★ 3.9k • written 10 weeks ago by
Xiao
• 0
0
votes
1
reply
335
views
DESeq2 interaction term + sva
sva
DESeq2
updated 10 weeks ago by
Michael Love
41k • written 3 months ago by
marinaw
▴ 20
0
votes
2
replies
285
views
combat output NaN
sva
4 months ago
maxixian1990
• 0
0
votes
2
replies
423
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
4 months ago
Crystal571
• 0
5
votes
2
replies
594
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
5 months ago
Federico
▴ 10
5
votes
8
replies
993
views
Batch correction and repeated measures
RUVSeq
sva
limma
written 5 months ago by
Jonathan
▴ 10
0
votes
1
reply
376
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
Shila
• 0
2
votes
3
replies
894
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
D-Bug
▴ 10
0
votes
2
replies
555
views
Fluidigm Data Batch Correction
sva
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Khushbu
• 0
2
votes
3
replies
753
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
8 months ago
amnahsiddiqa
• 0
2
votes
3
replies
995
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 8 months ago by
ATpoint
★ 3.9k • written 8 months ago by
amnahsiddiqa
• 0
0
votes
0
replies
348
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
8 months ago
amnahsiddiqa
• 0
0
votes
1
reply
485
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
marslena
• 0
2
votes
2
replies
775
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
13 months ago
Hatchet
• 0
5
votes
2
replies
717
views
Sva and batch effect
limma
BatchEffect
sva
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Lenny186
• 0
0
votes
2
replies
740
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
19 months ago
Marie
• 0
2
votes
9
replies
1.5k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
Jasmin
• 0
1
vote
0
replies
645
views
Why does surrogate variable confound with variable given in mod?
sva
20 months ago
shdam
▴ 10
1
vote
3
replies
1.3k
views
Error in shrinkage for DESeq2
sva
DESeq2
21 months ago
Kent
• 0
4
votes
3
replies
9.0k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 22 months ago by
wahaha
• 0 • written 6.4 years ago by
anton.kratz
▴ 60
1
vote
1
reply
705
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
ramonfallon
▴ 20
1
vote
2
replies
1.5k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
22 months ago
takemoto
• 0
0
votes
1
reply
843
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Mageiros
• 0
1
vote
1
reply
982
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 2.1 years ago by
ATpoint
★ 3.9k • written 2.1 years ago by
nhaus
▴ 10
1
vote
4
replies
1.6k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
2.1 years ago
Clay
• 0
0
votes
0
replies
1.0k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Bex
• 0
0
votes
5
replies
3.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.2 years ago by
ATpoint
★ 3.9k • written 3.0 years ago by
Xiaojie Cheng
• 0
0
votes
0
replies
751
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.5 years ago
georgia.katsoula
▴ 40
1
vote
4
replies
5.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
2.5 years ago
NewBioInfo
▴ 10
1
vote
2
replies
1.3k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
2.6 years ago
Ahdee
▴ 50
0
votes
1
reply
3.3k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 2.8 years ago by
chase.mateusiak
• 0 • written 6.9 years ago by
amoltej
▴ 10
0
votes
1
reply
1.5k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 2.8 years ago by
sebastian.lobentanzer
▴ 50 • written 2.8 years ago by
chiwut.wong
• 0
1
vote
4
replies
1.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 5 months ago by
Hamza
• 0 • written 3.0 years ago by
zeegzaag
• 0
0
votes
1
reply
1.2k
views
How to set mod0 in sva analysis
sva
updated 3.1 years ago by
Robert Castelo
★ 3.1k • written 3.1 years ago by
hank9cao
• 0
2
votes
2
replies
933
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 3.1 years ago by
ATpoint
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
0
votes
0
replies
917
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.2 years ago
epibio
▴ 10
1
vote
8
replies
1.4k
views
Error in running Combat function
sva
ComBat
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Reza
▴ 10
0
votes
5
replies
989
views
Variable of interest in combat correction
sva
combat
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
ch_el
▴ 10
0
votes
3
replies
997
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
jonellevillar
• 0
0
votes
10
replies
1.1k
views
Running SVA changes format of time variable in model
sva
proxitct
hms
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
jonellevillar
• 0
7
votes
6
replies
1.5k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 3.9 years ago by
W. Evan Johnson
▴ 850 • written 3.9 years ago by
Zach Roe
▴ 10
0
votes
1
reply
719
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Mozart
▴ 30
0
votes
1
reply
926
views
Adjusting for unwanted variation in DESeq2
DESeq2
deseq2
sva
rna-seq
differential expression anlaysis
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Nikolay Ivanov
• 0
1
vote
1
reply
905
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
whyw6948
• 0
2
votes
4
replies
995
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
rihards.saksis
• 0
1
vote
2
replies
882
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
vizio12341337
• 0
0
votes
0
replies
1.9k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
4.2 years ago
anne.bozack
• 0
0
votes
1
reply
832
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 4.3 years ago by
W. Evan Johnson
▴ 850 • written 4.3 years ago by
modarzi
▴ 10
50 results • Page
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Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Comment: BioC2024 abstract submission is open!
by
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• 0
What are the conditions for approval of people in difficult circumstances? I want this scholarship
Comment: European Bioconductor Conference 2023 planning
by
william
• 0
[@MariaDoyle][1] Without a doubt. In that position, I will be included in the discussion. [1]: https://support.bioconductor.org/u/239…
Comment: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
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• 0
Thank you for the detailed response. The code worked right away. I appreciate the quick response.
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
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Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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