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ComBat
•
reset
2
votes
6
replies
4.0k
views
Combat for batch effects
combat
9.1 years ago
zhouxiuqing
• 0
3
votes
4
replies
4.5k
views
Running Combat in SVA with NA values in matrix
sva
combat
8.4 years ago
CC
▴ 10
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2
combat
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
ribioinfo
▴ 100
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma
batch effect
ComBat
differential gene expression
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
svlachavas
▴ 830
0
votes
6
replies
5.9k
views
ComBat with multiple batches
sva
combat
450k
8.3 years ago
ben.run974
• 0
2
votes
5
replies
2.8k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 6.6 years ago by
W. Evan Johnson
▴ 850 • written 6.6 years ago by
JMallory
• 0
5
votes
3
replies
3.8k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
7.6 years ago
Bogdan
▴ 670
3
votes
8
replies
2.3k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 7.6 years ago by
manimaran_1975
▴ 30 • written 7.6 years ago by
Ewelina Dratkiewicz
• 0
7
votes
6
replies
1.6k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 4.0 years ago by
W. Evan Johnson
▴ 850 • written 4.0 years ago by
Zach Roe
▴ 10
1
vote
4
replies
3.5k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva
combat
8.8 years ago
GFM
▴ 20
7
votes
7
replies
8.3k
views
batch effect : comBat or blocking in limma ?
batch effect
combat
limma
block
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
eleonoregravier
▴ 70
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 7.9 years ago by
adam
• 0 • written 8.4 years ago by
AB
▴ 110
0
votes
2
replies
2.6k
views
Remove batch effect - condition partially confounded by data
combat
differential gene expression
sva
updated 9.2 years ago by
Jeff Leek
▴ 650 • written 9.3 years ago by
AdamJ
• 0
4
votes
4
replies
4.5k
views
sva::ComBat without covariate of interest?
sva
combat
updated 9.4 years ago by
W. Evan Johnson
▴ 850 • written 9.4 years ago by
Brent Pedersen
▴ 110
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Sam
▴ 10
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
2
votes
2
replies
3.6k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 9.4 years ago by
W. Evan Johnson
▴ 850 • written 9.4 years ago by
maren.lang
▴ 10
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.2 years ago by
Samuel Daniel
• 0 • written 4.5 years ago by
rajeshparmar4
▴ 10
10
votes
10
replies
4.0k
views
Method for batch correction
combat
sva
limma
updated 8.0 years ago by
Vegard Nygaard
▴ 110 • written 8.0 years ago by
AST
▴ 60
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva
combat
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
ch_el
▴ 10
0
votes
8
replies
2.3k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 6.4 years ago by
shaymaa_s_elgaafary
• 0 • written 8.7 years ago by
radhikaraheja
• 0
1
vote
3
replies
6.6k
views
Combat - error - system is computationally singular
combat
software error
rnaseq
complex-design
updated 9.5 years ago by
Peter Langfelder
★ 3.0k • written 9.5 years ago by
Stefano Mangiola
▴ 10
5
votes
2
replies
3.1k
views
ComBat - Including variable of interest in model matrix?
combat
sva
updated 9.5 years ago by
Jeff Leek
▴ 650 • written 9.5 years ago by
bengelmann
▴ 10
1
vote
1
reply
1.4k
views
ComBat (SVA) Application - Two Technical Effects
sva
ComBat
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 years ago by
andrew.j.skelton73
▴ 370
0
votes
4
replies
6.3k
views
ComBat: Error non-conformable arguments
ComBat
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
alison.sara.waller
• 0
0
votes
2
replies
5.4k
views
Combat in R (SVA package) error message
combat
software error
updated 8.9 years ago by
Peter Langfelder
★ 3.0k • written 8.9 years ago by
kimyoorin1
• 0
0
votes
6
replies
1.6k
views
Problem in analysing microarray data with ComBat
combat
updated 13 months ago by
W. Evan Johnson
▴ 850 • written 8.9 years ago by
melissa.sorci
• 0
2
votes
7
replies
2.1k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat
sva
8.9 years ago
edammer
• 0
0
votes
4
replies
1.4k
views
Reproducibility of results with ComBat
sva
combat
updated 8.7 years ago by
Jeff Leek
▴ 650 • written 8.7 years ago by
anne.bozack
• 0
1
vote
1
reply
2.6k
views
sva and svaseq for unsupervised analysis of expression data
sva
combat
gene expression
batch effect
rnaseq
updated 8.6 years ago by
Jeff Leek
▴ 650 • written 8.6 years ago by
Farshad Farshidfar
▴ 10
1
vote
1
reply
4.9k
views
Combat generating negative values, should I log2 transform first?
combat
batch effect
updated 8.5 years ago by
W. Evan Johnson
▴ 850 • written 8.5 years ago by
Ahdee
▴ 50
0
votes
2
replies
3.4k
views
Using sva ComBat on DESeq2 Data
deseq2
DE
rnaseq
sva
combat
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
mbio.kyle
• 0
1
vote
2
replies
1.9k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat
diagnostic plot
batch effect
affymetrix microarrays
sva
updated 8.2 years ago by
W. Evan Johnson
▴ 850 • written 8.2 years ago by
svlachavas
▴ 830
7
votes
3
replies
3.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva
SVA
sva
ComBat
batch effect
updated 8.0 years ago by
W. Evan Johnson
▴ 850 • written 8.0 years ago by
John Townsend
▴ 20
2
votes
3
replies
1.4k
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 8.0 years ago by
chris86
▴ 420 • written 8.0 years ago by
TP
• 0
0
votes
1
reply
1.3k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray
batcheffectcorrection
affymetrix microarrays
ComBat
sva
updated 7.8 years ago by
chris86
▴ 420 • written 7.8 years ago by
svlachavas
▴ 830
0
votes
2
replies
1.4k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
grimmerucsf
• 0
3
votes
12
replies
3.1k
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
hackingfactory
▴ 10
4
votes
16
replies
4.5k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
joseale2310
▴ 10
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
Bogdan
▴ 670
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 4.7 years ago by
Andrew_McDavid
▴ 270 • written 4.7 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.1k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
ege.dedeoglu
• 0
2
votes
3
replies
1.0k
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 4.7 years ago by
swbarnes2
★ 1.3k • written 4.7 years ago by
ag1805x
▴ 80
0
votes
1
reply
960
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.4 years ago by
lucasmiranda42
• 0
0
votes
1
reply
878
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 4.4 years ago by
W. Evan Johnson
▴ 850 • written 4.4 years ago by
modarzi
▴ 10
1
vote
2
replies
921
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
vizio12341337
• 0
0
votes
3
replies
1.0k
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
jonellevillar
• 0
1
vote
8
replies
1.4k
views
Error in running Combat function
sva
ComBat
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
Reza
▴ 10
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 6 months ago by
Hamza
• 0 • written 3.1 years ago by
zeegzaag
• 0
1
vote
4
replies
5.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
2.6 years ago
NewBioInfo
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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