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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
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
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
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
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
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
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
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
0
votes
8
replies
6.6k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2
PCA
batch effect
6.8 years ago
pkachroo
▴ 10
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
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
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
1
vote
1
reply
4.9k
views
Combat generating negative values, should I log2 transform first?
combat
batch effect
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
Ahdee
▴ 50
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
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
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
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
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.7 years ago
Pietro
▴ 40
2
votes
5
replies
4.2k
views
Batch Effect Correction
batch effect
removebatcheffect
edgeR
rld
DEseq2
5.8 years ago
Antonio Ahn
▴ 10
4
votes
7
replies
3.8k
views
removeBatchEffect -- warnings and results
batch effect
edgeR
8.6 years ago
pavlidisp
▴ 10
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
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
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
1
vote
4
replies
3.4k
views
Looking for Batch effects in PCA
batch effect
pca
5.8 years ago • updated 15 months ago
KB
▴ 50
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
5
replies
3.2k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect
limma
rna seq
DE
updated 4.0 years ago by
Steve Lianoglou
★ 13k • written 4.0 years ago by
svlachavas
▴ 830
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
1
vote
3
replies
3.2k
views
Batch effect removal with Deseq2
deseq2
batch effect
removebatcheffect()
limma
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
lirongrossmann
▴ 80
3
votes
4
replies
3.1k
views
Single cells batch effects
RUV
single cell
batch effect
7.1 years ago
ribioinfo
▴ 100
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
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
1
vote
2
replies
2.9k
views
Problem with n.sv in sva package
batch effect
sva
8.7 years ago
daih
• 0
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
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
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
1
vote
4
replies
2.7k
views
Remove batch effect using individuals as random in the model in Limma
batch effect
Coeficents non estimable
block
random effects
limma design matrix
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mheydarpour
▴ 10
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
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 8.7 years ago by
Farshad Farshidfar
▴ 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
1
vote
6
replies
2.4k
views
limma + voom + sva + complex RNA-seq design?
limma
sva
batch effect
7.4 years ago
irenegallego
• 0
0
votes
4
replies
2.4k
views
deseq2 correction batch effect without design
deseq2
batch effect
updated 4.8 years ago by
swbarnes2
★ 1.3k • written 4.8 years ago by
mdidish
• 0
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 4.2 years ago by
swbarnes2
★ 1.3k • written 4.2 years ago by
l.rijnberk
• 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
1
vote
2
replies
2.2k
views
keep getting this error "number of rows is not the same across batches" even though my 2 matrices have the same row number
mnncorrect
batch effect
scran
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
sara.nejat
• 0
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
1
vote
4
replies
2.0k
views
model matrix for edgeR paired-design with batch effect
edgeR
paired samples
batch effect
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
NGS-seeker
• 0
0
votes
3
replies
2.0k
views
Query about DEXSeq
dexseq
batch effect
PCA
8.7 years ago • updated 8.6 years ago
n.deshpande
• 0
2
votes
14
replies
1.9k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq
batch effect
deseq2
edger
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
rproendo
▴ 20
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
0
votes
6
replies
1.9k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2
batch effect
RNAseq
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
chudar.chudar
▴ 30
50 results • Page
1 of 1
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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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