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Showing :
batch effect
•
reset
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
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
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
10
votes
18
replies
16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
4.9 years ago
Mozart
▴ 30
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva
batch effect
rnaseq
removebatcheffect()
limma
updated 8.5 years ago by
Jeff Leek
▴ 650 • written 8.5 years ago by
AB
▴ 110
8
votes
14
replies
2.8k
views
Batch with only one sample or condition
limma
batch effect
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
eleonoregravier
▴ 70
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
updated 4.9 years ago by
Victoria
• 0 • written 5.6 years ago by
Laura
▴ 20
7
votes
13
replies
1.9k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma
microarray
hugeneST
batch effect
DE
updated 5.3 years ago by
Ryan C. Thompson
★ 7.9k • written 5.3 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
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
6
votes
3
replies
6.9k
views
deseq2 correcting for batch effects
deseq2
batch effect
removebatcheffect()
design matrix
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
Assa Yeroslaviz
★ 1.5k
6
votes
4
replies
1.5k
views
limma batch question
limma
batch effect
7.3 years ago
jalali4
• 0
6
votes
4
replies
1.4k
views
Combining newer/older RNAseq data, batch correcting
rnaseq
limma
sva
batch effect
voom
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
schrist1
▴ 10
6
votes
7
replies
3.6k
views
Batch Correction with only one sample in a batch
batch effect
deseq2
limma
updated 6.0 years ago by
Ryan C. Thompson
★ 7.9k • written 6.0 years ago by
i.sudbery
▴ 40
6
votes
11
replies
5.8k
views
Limma, blocking batch effect
limma
batch effect
updated 8.8 years ago by
svlachavas
▴ 830 • written 8.8 years ago by
Jeannette
▴ 20
6
votes
9
replies
1.6k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma
illumina
microarray
multifactorial design
batch effect
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Konstantinos Yeles
▴ 80
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment
scran
sequencing depth
batch effect
scrnaseq
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
liam.salleh
• 0
6
votes
5
replies
4.2k
views
voom + removeBatchEffect + gene clustering
voom
limma
clustering
removebatcheffect()
batch effect
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
ale.breschi
▴ 10
6
votes
6
replies
5.4k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva
deseq2
batch effect
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
wariobrega
• 0
5
votes
13
replies
2.7k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2
DEG
ANOVA
Batch effect
Comparison
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
amin.ghareyazi
• 0
5
votes
1
reply
1.2k
views
Limma - Using removeBatchEffect before differential expression analysis
limma
batch effect
differential expression
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
jmoon1194
• 0
5
votes
3
replies
1.2k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger
limma
duplicateCorrelation
batch effect
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
altintas.ali
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
4
votes
12
replies
4.7k
views
remove batch effect using limma
limma
rnaseq
batch effect
pearsoncorrelation
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
elpsakkas
• 0
4
votes
7
replies
3.8k
views
removeBatchEffect -- warnings and results
batch effect
edgeR
8.6 years ago
pavlidisp
▴ 10
4
votes
3
replies
1.1k
views
EdgeR: is more than one control per batch an issue?
edgeR
batch effect
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Ekarl2
▴ 80
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect
single cells
mnnCorrect
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
xingxd16
▴ 20
4
votes
5
replies
2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model
batch effect
DESeq2
design
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
tim.meese
• 0
3
votes
12
replies
3.2k
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
3
votes
2
replies
10k
views
Batch effect removal in edgeR
edger
batch effect
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
candida.vaz
▴ 50
3
votes
12
replies
4.7k
views
Batch correction when only some subjects have replicates across batches
limma
batch effect
rna-seq
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
Mike A
▴ 10
3
votes
2
replies
7.8k
views
Problem with coefficients that are not estimable (limma)
limma
batch effect
updated 3.0 years ago by
rf
• 0 • written 5.8 years ago by
rrm38
• 0
3
votes
2
replies
1.1k
views
Using deseq2 with batch effects and classification as downstream analysis
deseq2
batch effect
classification
updated 5.5 years ago by
Michael Love
41k • written 5.6 years ago by
Maryam
• 0
3
votes
3
replies
1.4k
views
Difficulties with probable batch effect in paired blocked (treatment and placebo) experiment
deseq2
edger
limma
batch effect
paired design
6.1 years ago
Vladimir Krasikov
▴ 90
3
votes
19
replies
3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.1 years ago
mheydarpour
▴ 10
3
votes
2
replies
1.8k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq
deseq2
differential expression
batch effect
replicates
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
Nik dAK
▴ 10
3
votes
4
replies
3.1k
views
Single cells batch effects
RUV
single cell
batch effect
7.1 years ago
ribioinfo
▴ 100
3
votes
8
replies
2.8k
views
Batch effects in limma
limma
batch effect
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
smt8n
• 0
3
votes
7
replies
4.9k
views
limma::removeBatchEffect into DESeq2
deseq2
limma
batch effect
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Patricia
• 0
2
votes
8
replies
3.3k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
bioyas
▴ 10
2
votes
2
replies
2.5k
views
order of covariates for GLM with edgeR
edger
differential expression
covariate
batch effect
glm
updated 8.3 years ago by
Gordon Smyth
50k • written 8.4 years ago by
aec
▴ 90
2
votes
2
replies
1.6k
views
Different DEG results using Ballgown and edgeR
edger
ballgown
rnaseq
batch effect
adjustvars
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
IRAIA.MAIALEN
• 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
2
votes
1
reply
930
views
Plotting Gene Expression Data From Multiple Batches
batch effect
microarray
plot
updated 6.8 years ago by
Jenny Drnevich
★ 2.0k • written 6.8 years ago by
tcalvo
▴ 90
2
votes
5
replies
4.2k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
5.8 years ago
Antonio Ahn
▴ 10
2
votes
1
reply
896
views
Batch Variation-MDS Plot
edger
R
batch effect
updated 5.8 years ago by
Gordon Smyth
50k • written 5.9 years ago by
drskm7
• 0
2
votes
1
reply
1.0k
views
gene expression data analysis and batch effect methods
batch effect
gene expression
updated 6.9 years ago by
chris86
▴ 420 • written 6.9 years ago by
tati6406
• 0
2
votes
1
reply
2.3k
views
Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma
batch effect
rna-seq
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
adscheid3
• 0
2
votes
5
replies
1.4k
views
Compare groups of different RNAseq sets
batch effect
limma
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
b.nota
▴ 360
2
votes
1
reply
2.0k
views
differential expressed genes, paired samples and multiple factors
edgeR
batch effect
differential gene expression
paired samples
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
pavlidisp
▴ 10
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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