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sva
•
reset
0
votes
0
replies
33
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
1 day ago
Shaimaa Gamal
• 0
1
vote
1
reply
770
views
ComBat with repeated measures
ComBat
sva
updated 25 days ago by
ATpoint
★ 4.8k • written 25 days ago by
s20
• 0
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
9 weeks ago
bbao
▴ 10
0
votes
2
replies
610
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
Lina
▴ 10
0
votes
3
replies
733
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
6 months ago
Travis
• 0
4
votes
5
replies
12k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 8 months ago by
ndphuc1605
• 0 • written 7.5 years ago by
anton.kratz
▴ 60
0
votes
4
replies
1.2k
views
Generating surrogate variables across multiple variables of interest
sva
9 months ago • updated 8 months ago
Robert
• 0
0
votes
3
replies
1.3k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 12 months ago by
W. Evan Johnson
▴ 870 • written 12 months ago by
schlumbohm
• 0
3
votes
6
replies
1.2k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
12 months ago
nhaus
▴ 70
0
votes
2
replies
578
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
12 months ago
michelafrancesconi8
• 0
0
votes
4
replies
1.1k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
12 months ago
Lucy
▴ 60
0
votes
8
replies
1.1k
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
13 months ago
michelafrancesconi8
• 0
0
votes
3
replies
716
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
MEME
▴ 10
0
votes
5
replies
1.6k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 15 months ago by
ATpoint
★ 4.8k • written 15 months ago by
Xiao
• 0
0
votes
1
reply
831
views
DESeq2 interaction term + sva
sva
DESeq2
updated 15 months ago by
Michael Love
43k • written 16 months ago by
marinaw
▴ 20
0
votes
2
replies
706
views
combat output NaN
sva
17 months ago
maxixian1990
• 0
0
votes
4
replies
1.2k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 12 months ago by
Michael Love
43k • written 18 months ago by
Crystal571
• 0
5
votes
2
replies
2.3k
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
19 months ago
Federico
▴ 10
5
votes
9
replies
2.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 12 months ago by
Gordon Smyth
52k • written 19 months ago by
Jonathan
▴ 10
0
votes
1
reply
866
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Shila
• 0
2
votes
3
replies
2.6k
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 20 months ago by
James W. MacDonald
68k • written 20 months ago by
D-Bug
▴ 10
0
votes
2
replies
991
views
Fluidigm Data Batch Correction
sva
limma
updated 21 months ago by
Gordon Smyth
52k • written 21 months ago by
Khushbu
• 0
3
votes
3
replies
2.2k
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
22 months ago
amnahsiddiqa
▴ 10
2
votes
3
replies
2.3k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 22 months ago by
ATpoint
★ 4.8k • written 22 months ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
683
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
22 months ago
amnahsiddiqa
▴ 10
0
votes
1
reply
888
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 2.1 years ago by
ATpoint
★ 4.8k • written 2.1 years ago by
marslena
• 0
2
votes
2
replies
1.2k
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
2.2 years ago
Hatchet
• 0
5
votes
2
replies
1.2k
views
Sva and batch effect
limma
BatchEffect
sva
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 years ago by
Lenny186
• 0
0
votes
2
replies
1.2k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
2.7 years ago
Marie
• 0
2
votes
9
replies
2.3k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.7 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Jasmin
• 0
1
vote
0
replies
897
views
Why does surrogate variable confound with variable given in mod?
sva
2.8 years ago
shdam
▴ 10
1
vote
3
replies
1.8k
views
Error in shrinkage for DESeq2
sva
DESeq2
2.9 years ago
Kent
• 0
1
vote
1
reply
1.0k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
ramonfallon
▴ 20
1
vote
2
replies
2.3k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
2.9 years ago
takemoto
• 0
0
votes
1
reply
1.6k
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 3.0 years ago by
Gordon Smyth
52k • written 3.0 years ago by
Mageiros
• 0
1
vote
1
reply
1.7k
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 3.2 years ago by
ATpoint
★ 4.8k • written 3.2 years ago by
nhaus
▴ 70
1
vote
4
replies
2.3k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
3.2 years ago
Clay
• 0
0
votes
0
replies
1.4k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
Bex
• 0
0
votes
5
replies
5.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 3.3 years ago by
ATpoint
★ 4.8k • written 4.1 years ago by
Xiaojie Cheng
• 0
0
votes
0
replies
1.1k
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
3.6 years ago
georgia.katsoula
▴ 40
1
vote
4
replies
8.0k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
3.6 years ago
NewBioInfo
▴ 10
1
vote
2
replies
1.9k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
3.7 years ago
Ahdee
▴ 60
0
votes
1
reply
4.1k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 3.9 years ago by
chase.mateusiak
• 0 • written 8.0 years ago by
amoltej
▴ 10
0
votes
1
reply
2.4k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 3.9 years ago by
sebastian.lobentanzer
▴ 60 • written 3.9 years ago by
chiwut.wong
• 0
1
vote
4
replies
3.2k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 18 months ago by
Hamza
• 0 • written 4.1 years ago by
zeegzaag
• 0
0
votes
1
reply
1.9k
views
How to set mod0 in sva analysis
sva
updated 4.2 years ago by
Robert Castelo
★ 3.4k • written 4.2 years ago by
hank9cao
• 0
2
votes
2
replies
1.4k
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 4.2 years ago by
ATpoint
★ 4.8k • written 4.2 years ago by
MOHAMMAD
• 0
0
votes
0
replies
1.2k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
4.3 years ago
epibio
▴ 10
1
vote
8
replies
2.0k
views
Error in running Combat function
sva
ComBat
updated 4.2 years ago by
Kevin Blighe
★ 4.0k • written 4.3 years ago by
Reza
▴ 10
0
votes
5
replies
1.5k
views
Variable of interest in combat correction
sva
combat
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
ch_el
▴ 10
50 results • Page
1 of 1
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Replies
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Leonardo Collado Torres
★ 1.1k
Thanks for the answer James! I had forgotten about the "PM" part of CPM when I met with Kinnary yesterday!
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Leonardo Collado Torres
★ 1.1k
Thank you Gordon for the detailed answer, examples, and link to the unpublished thesis!
Answer: Make DEXSeq plot normal scale
by
James W. MacDonald
68k
It's hard coded, so you will not be able to change the vertical axis of the top plot without getting the code and modifying. You can simply…
Answer: RNA Seq using Lrt
by
James W. MacDonald
68k
When you perform an LRT, you are testing the coefficients that are no longer included in the reduced model. So you are testing to see if in…
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Gordon Smyth
52k
Mmm, I am not at all attracted to those approaches. Perhaps the use of `log(cpm+1)` might facilitate the use of sparse methods in other pac…
Votes
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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