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 :
limma
•
reset
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 19 days ago
Chris
▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
29 days ago • updated 18 days ago
Chris
▴ 10
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.3 years ago by
tleona3
• 0
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 5 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
8
votes
6
replies
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Amit
• 0
7
votes
6
replies
482
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
7
votes
2
replies
865
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
6
votes
7
replies
798
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Jonathan
▴ 10
6
votes
5
replies
6.4k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 8 months ago by
Gordon Smyth
50k • written 2.5 years ago by
David Lyon
▴ 340
5
votes
3
replies
317
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.2 years ago by
r.i.s.alnuwaysir
▴ 10
5
votes
2
replies
703
views
PhD student
TMM
limma
10 months ago
Nisha
• 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 27 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
5
votes
5
replies
827
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
9 months ago
Jitendra
▴ 10
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 7 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Amit
• 0
5
votes
25
replies
993
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jitendra
▴ 10
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 5 months ago by
Shaimaa Gamal
• 0 • written 12 months ago by
pg45863
▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
3
replies
723
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Gerhard Thallinger
▴ 180
5
votes
2
replies
607
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by
Gordon Smyth
50k • written 8.0 years ago by
nathan
• 0
4
votes
6
replies
653
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
Shaimaa Gamal
• 0
4
votes
3
replies
385
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
4
votes
5
replies
893
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by
Gordon Smyth
50k • written 8 months ago by
Jonathan
▴ 10
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Jonathan
▴ 10
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
8 months ago
Ethan Nguyen
• 0
3
votes
3
replies
595
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
stuartthafass
• 0
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata
limma
8 months ago • updated 5 months ago
triZZla
• 0
3
votes
2
replies
322
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
3 months ago
Shaimaa Gamal
• 0
3
votes
3
replies
988
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
10 months ago
amnahsiddiqa
▴ 10
3
votes
4
replies
563
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
3
votes
10
replies
478
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
Abbey
• 0
3
votes
8
replies
545
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago
dl17032000
• 0
3
votes
11
replies
2.6k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
12 months ago • updated 11 months ago
Anna
▴ 20
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 12 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
alexia.brunel
• 0
3
votes
5
replies
932
views
limma-trend vs. limma-voom theoretical difference
limma
limma-trend
limma-voom
updated 4 months ago by
floriandeckert
▴ 30 • written 18 months ago by
hainct
• 0
3
votes
2
replies
465
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
S
• 0
3
votes
5
replies
673
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
3
votes
6
replies
862
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA
limma
19 days ago
Chris
▴ 10
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
D-Bug
▴ 10
2
votes
2
replies
306
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
3 months ago
SamGG
▴ 350
2
votes
1
reply
314
views
removeBatchEffect with non-linear model fit
limma
DESeq2
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
georgii.vdovin
• 0
2
votes
1
reply
880
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor
biocon
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
ningyuan
• 0
2
votes
8
replies
568
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
2
votes
1
reply
281
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 12 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
6 months ago
Tyler Sagendorf
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
Good day ATpoint, Could you pls advise also ehy this error could happened design contains one or more variables with all samples having t…
Comment: How to run allelic imbalance in apeglm
by
euge.eugenio
▴ 20
@mikelove could you help me? Thanks!
Comment: ENCORI or starBase : ceRNA data retrieval using Web API and curl
by
ATpoint
★ 4.1k
This is not related to Bioconductor. Biostars is more suited where you posted already.
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards
• All
Popular Question
to
shepherl
3.9k
Popular Question
to
Hussain
• 0
Popular Question
to
euge.eugenio
▴ 20
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Locations
• All
United States,
2 minutes ago
Wageningen University, Wageningen, the Netherlands,
2 minutes ago
United States,
7 minutes ago
United States,
10 minutes ago
Denver, University of Colorado Anschutz Medical Campus,
30 minutes ago
Traffic: 729 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