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Showing :
Limma
•
reset
1
vote
2
replies
753
views
contrast matrix design for a continuous variable
limma
13 months ago • updated 11 months ago
dtzhu337
• 0
3
votes
3
replies
1.1k
views
Crossover design with limma
limma
crossover
updated 12 months ago by
Gordon Smyth
53k • written 13 months ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
1.8k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
abadgerw
• 0
6
votes
10
replies
3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
mohammedtoufiq91
▴ 10
1
vote
3
replies
840
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 13 months ago by
Melisa Tecik
• 0
0
votes
2
replies
430
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
13 months ago
giulia.gentile
▴ 10
4
votes
2
replies
1.4k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Ahdee
▴ 60
1
vote
2
replies
539
views
Limma Interaction Effect with Covariates
limma
DMRcate
13 months ago
kitzhu
• 0
2
votes
3
replies
1.4k
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 13 months ago by
Gordon Smyth
53k • written 14 months ago by
kyj2226
• 0
3
votes
4
replies
1.2k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
14 months ago • updated 13 months ago
dseauer
• 0
1
vote
3
replies
931
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
14 months ago • updated 13 months ago
abadgerw
• 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
14 months ago • updated 13 months ago
abadgerw
• 0
1
vote
8
replies
2.6k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 14 months ago by
Adam Marstrand
• 0
1
vote
2
replies
1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
14 months ago
Ai
• 0
3
votes
3
replies
1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 14 months ago by
Satoshi
• 0
4
votes
3
replies
1.2k
views
Analysis of 2*4 factorial design
limma
updated 14 months ago by
Gordon Smyth
53k • written 14 months ago by
Sudipta
• 0
2
votes
12
replies
2.8k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
14 months ago • updated 13 months ago
john
• 0
4
votes
6
replies
2.0k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 14 months ago by
Gordon Smyth
53k • written 14 months ago by
abadgerw
• 0
4
votes
6
replies
1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
14 months ago
altintas.ali
• 0
2
votes
2
replies
972
views
Automatically generate contrasts from a model matrix / formula
limma
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Jonathan
▴ 10
3
votes
3
replies
803
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
15 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
788
views
Need help interpreting heatmaps from limma
limma
written 15 months ago by
lhwh1208
• 0
2
votes
1
reply
2.0k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
danphillips28
▴ 10
5
votes
4
replies
1.1k
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
Bioinformagician
• 0
1
vote
2
replies
936
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Ben
▴ 10
0
votes
0
replies
499
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
15 months ago
tim.meese
• 0
0
votes
2
replies
838
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
blmurphy
• 0
0
votes
2
replies
739
views
Question on performing ANOVA-like analysis using limma
limma
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
grubble
• 0
17
votes
9
replies
8.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 15 months ago by
James W. MacDonald
68k • written 9.6 years ago by
ompandey
▴ 10
2
votes
1
reply
787
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
rae.alshammari
▴ 20
0
votes
1
reply
2.3k
views
Unable to install/use limma
limma
Bioconductor
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
Jennifer
• 0
3
votes
3
replies
987
views
voom does not seem to properly correct for library size
limma
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
ATpoint
★ 5.0k
1
vote
5
replies
1.5k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Xuan Yi
• 0
0
votes
3
replies
1.0k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2
limma
DifferentialExpression
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Jiahao Tian
• 0
3
votes
4
replies
1.4k
views
using limma trend workflow in CAMERA
CAMERA
limma
17 months ago • updated 16 months ago
Jiahao Tian
• 0
3
votes
3
replies
1.0k
views
One-sided tests with CAMERA-PR
CAMERA
limma
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Tyler Sagendorf
▴ 10
1
vote
6
replies
1.3k
views
limma and Syntactically Invalid Factor Values
limma
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
1.1k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
17 months ago
Bioinformagician
• 0
5
votes
3
replies
1.1k
views
Limma comparing gene expression between base line and one treatment
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
AL
• 0
0
votes
1
reply
1.2k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
picasa1983
• 0
2
votes
5
replies
1.2k
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
sop
• 0
4
votes
14
replies
2.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 17 months ago by
Gordon Smyth
53k • written 18 months ago by
Michael E
• 0
3
votes
4
replies
1.3k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
18 months ago
jcollier
• 0
4
votes
4
replies
1.8k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
18 months ago
sukeshinik5
▴ 20
0
votes
1
reply
599
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Neha
• 0
4
votes
4
replies
1.2k
views
Warning message when running limma with covariates
limma
18 months ago • updated 12 months ago
Chris
▴ 20
0
votes
8
replies
2.3k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix
limma
18 months ago
jiachengd
• 0
5
votes
5
replies
1.8k
views
Limma with covariates
limma
written 18 months ago by
Chris
▴ 20
3
votes
13
replies
2.1k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq
limma
updated 19 months ago by
Masongeorge
• 0 • written 19 months ago by
ij283
• 0
3
votes
2
replies
1.3k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
19 months ago
mohammedtoufiq91
▴ 10
4,228 results • Page
2 of 85
Recent ...
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Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
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