Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
4
votes
7
replies
3.8k
views
removeBatchEffect -- warnings and results
batch effect
edgeR
8.6 years ago
pavlidisp
▴ 10
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
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
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
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
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
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
6
replies
1.1k
views
DESeq2: Error when correcting batch effect
deseq2
batch effect
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Rimma
• 0
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
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
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
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
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
1
vote
5
replies
999
views
differential expression analysis in edgeR when you have 2 experiments and batch effect in 1 of the 2 experiments.
edger
batch effect
differential expression
7.6 years ago
sezimmer
• 0
1
vote
5
replies
1.2k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2
rna-seq
illumina
batch effect
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
JP Carter
▴ 40
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
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
4
replies
1.0k
views
Batch effect and edgeR analysis
batch effect
edgeR
RNA-seq
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
Sara
▴ 10
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
3
votes
4
replies
3.1k
views
Single cells batch effects
RUV
single cell
batch effect
7.1 years ago
ribioinfo
▴ 100
6
votes
4
replies
1.5k
views
limma batch question
limma
batch effect
7.3 years ago
jalali4
• 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
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
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
1
vote
4
replies
1.6k
views
edgeR design matrix for 2 variables + batch effect
egdeR
design matrix
batch effect
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
ahsindoomilup
• 0
1
vote
4
replies
1.5k
views
Normalized counts after fitting linear model with batch effects - edgeR
edger
batch effect
normalized counts
updated 6.3 years ago by
Ryan C. Thompson
★ 7.9k • written 6.3 years ago by
Yahan
• 0
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
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
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
50 results • Page
1 of 1
Recent ...
Replies
Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
James W. MacDonald
65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
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
Awards
• All
Popular Question
to
Ian D.
▴ 70
Popular Question
to
junhui.li11
• 0
Scholar
to
James W. MacDonald
65k
Popular Question
to
jeffrey.maurer
• 0
Centurion
to
Chris
• 0
Locations
• All
India,
2 minutes ago
Switzerland,
3 minutes ago
Switzerland,
5 minutes ago
UPF, Barcelona, Spain,
6 minutes ago
Italy,
7 minutes ago
Traffic: 598 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6