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SVA
•
reset
1
vote
1
reply
58
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
3 days ago • updated 2 days ago
takemoto
• 0
0
votes
1
reply
92
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 5 weeks ago by
Gordon Smyth
45k • written 5 weeks ago by
Mageiros
• 0
1
vote
1
reply
176
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 12 weeks ago by
ATpoint
★ 1.2k • written 12 weeks ago by
nhaus
• 0
1
vote
4
replies
330
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
3 months ago • updated 12 weeks ago
Clay
• 0
0
votes
0
replies
228
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 4 months ago by
James W. MacDonald
59k • written 4 months ago by
Bex
• 0
0
votes
5
replies
1.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 4 months ago by
ATpoint
★ 1.2k • written 14 months ago by
Xiaojie Cheng
• 0
0
votes
0
replies
238
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
7 months ago
georgia.katsoula
▴ 40
0
votes
4
replies
1.1k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
8 months ago
NewBioInfo
• 0
1
vote
2
replies
344
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
9 months ago
Ahdee
▴ 50
0
votes
1
reply
2.4k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 12 months ago by
chase.mateusiak
• 0 • written 5.1 years ago by
amoltej
▴ 10
0
votes
1
reply
507
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 12 months ago by
sebastian.lobentanzer
▴ 50 • written 12 months ago by
chiwut.wong
• 0
1
vote
3
replies
428
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 14 months ago by
Kevin Blighe
3.5k • written 14 months ago by
zeegzaag
• 0
0
votes
1
reply
413
views
How to set mod0 in sva analysis
sva
updated 15 months ago by
Robert Castelo
★ 2.8k • written 15 months ago by
hank9cao
• 0
2
votes
2
replies
362
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 15 months ago by
ATpoint
★ 1.2k • written 15 months ago by
MOHAMMAD
• 0
0
votes
0
replies
414
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
16 months ago
epibio
▴ 10
1
vote
8
replies
548
views
Error in running Combat function
sva
ComBat
updated 16 months ago by
Kevin Blighe
3.5k • written 16 months ago by
Reza
▴ 10
0
votes
5
replies
400
views
Variable of interest in combat correction
sva
combat
updated 18 months ago by
James W. MacDonald
59k • written 18 months ago by
ch_el
▴ 10
0
votes
3
replies
362
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 19 months ago by
Kevin Blighe
3.5k • written 20 months ago by
jonellevillar
• 0
0
votes
10
replies
466
views
Running SVA changes format of time variable in model
sva
proxitct
hms
updated 20 months ago by
James W. MacDonald
59k • written 20 months ago by
jonellevillar
• 0
7
votes
6
replies
497
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 2.0 years ago by
W. Evan Johnson
▴ 840 • written 2.0 years ago by
Zach Roe
▴ 10
0
votes
1
reply
249
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 2.1 years ago by
James W. MacDonald
59k • written 2.1 years ago by
Mozart
▴ 20
0
votes
1
reply
240
views
Adjusting for unwanted variation in DESeq2
DESeq2
deseq2
sva
rna-seq
differential expression anlaysis
updated 2.2 years ago by
James W. MacDonald
59k • written 2.2 years ago by
Nikolay Ivanov
• 0
1
vote
1
reply
320
views
SVA paired samples
SVA
EPIC
methylation
limma
updated 2.2 years ago by
James W. MacDonald
59k • written 2.2 years ago by
whyw6948
• 0
2
votes
4
replies
399
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 2.3 years ago by
Michael Love
37k • written 2.3 years ago by
rihards.saksis
• 0
1
vote
2
replies
338
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 2.3 years ago by
Gordon Smyth
45k • written 2.3 years ago by
vizio12341337
• 0
0
votes
0
replies
811
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
2.4 years ago
anne.bozack
• 0
0
votes
1
reply
362
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 2.5 years ago by
W. Evan Johnson
▴ 840 • written 2.5 years ago by
modarzi
▴ 10
0
votes
0
replies
326
views
limma-voom group design and its effect on sva
limma
voom
group-design
sva
2.5 years ago
kentfung
• 0
0
votes
8
replies
493
views
Error in sva() function: missing values, NaNs produced
sva
batch-correction
updated 2.5 years ago by
James W. MacDonald
59k • written 2.5 years ago by
thkapell
▴ 10
0
votes
3
replies
419
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 2.6 years ago by
Martin Morgan
25k • written 2.6 years ago by
dhwani2410
• 0
2
votes
5
replies
573
views
SVA for repeated measures design
SVA
deseq2
repeated measures
updated 2.6 years ago by
Robert Castelo
★ 2.8k • written 2.7 years ago by
sara.blocquiaux
• 0
0
votes
1
reply
445
views
Handling adjustment variables and surrogate variables in model
sva
deseq2
updated 2.7 years ago by
James W. MacDonald
59k • written 2.7 years ago by
rbutler
• 0
1
vote
1
reply
459
views
Bioconductor SVA: two variables of interest
sva
updated 2.7 years ago by
James W. MacDonald
59k • written 2.7 years ago by
sara.blocquiaux
• 0
4
votes
5
replies
416
views
Design matrix with intercept for multiple cluster comparison
limma
sva
updated 2.7 years ago by
centralmenu10
• 0 • written 2.7 years ago by
kentfung
• 0
0
votes
2
replies
387
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
ege.dedeoglu
• 0
0
votes
3
replies
352
views
Design matrix for cohort with samples outside "block"
limma
voom
sva
2.8 years ago
kentfung
• 0
0
votes
0
replies
260
views
fsva function does not work without newdat argument
sva
2.8 years ago
jakob.wirbel
• 0
0
votes
0
replies
345
views
The correct specification of the model matrix to ComBat
ComBat
sva
2.8 years ago
Sam
▴ 10
7
votes
4
replies
2.4k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 2.8 years ago by
Gordon Smyth
45k • written 2.8 years ago by
Bogdan
▴ 640
0
votes
0
replies
471
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
2.9 years ago
kentfung
• 0
0
votes
1
reply
525
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq
sva
DSS
updated 2.9 years ago by
keegan
▴ 60 • written 2.9 years ago by
gjl
• 0
2
votes
8
replies
1.2k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
bioyas
▴ 10
2
votes
1
reply
743
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
3.0 years ago
epibio
▴ 10
5
votes
3
replies
945
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 3.0 years ago by
Peter Langfelder
★ 2.6k • written 3.0 years ago by
mikhael.manurung
▴ 240
0
votes
1
reply
388
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 3.1 years ago by
Michael Love
37k • written 3.1 years ago by
Mozart
▴ 20
3
votes
12
replies
1.5k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 3.1 years ago by
James W. MacDonald
59k • written 3.1 years ago by
hackingfactory
▴ 10
1
vote
1
reply
446
views
svaseq - over adjustment
svaseq
sva
3.2 years ago
flippy23
• 0
0
votes
8
replies
641
views
Computationally Singular Matrices - DESeq
deseq2
rnaseq
sva
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
flippy23
• 0
1
vote
2
replies
670
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 3.2 years ago by
Gosia Nowicka
▴ 90 • written 3.3 years ago by
maya.kappil
▴ 20
4
votes
4
replies
899
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 3.3 years ago by
Gordon Smyth
45k • written 3.3 years ago by
enricoferrero
▴ 610
50 results • Page
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Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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