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Showing :
Limma
•
reset
0
votes
2
replies
196
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
4 days ago • updated 3 days ago
Tadeoye
▴ 20
0
votes
2
replies
400
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 7 days ago by
Gordon Smyth
52k • written 8 days ago by
Lina
▴ 10
2
votes
3
replies
1.1k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 8 days ago by
James W. MacDonald
67k • written 9 days ago by
giulia.gentile
▴ 10
1
vote
2
replies
270
views
contrast matrix design for a continuous variable
limma
11 days ago
dtzhu337
• 0
3
votes
3
replies
520
views
Crossover design with limma
limma
crossover
16 days ago • updated 9 days ago
Marek Gierlinski
▴ 30
0
votes
9
replies
720
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 8 days ago by
James W. MacDonald
67k • written 14 days ago by
abadgerw
• 0
6
votes
10
replies
2.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 4 days ago by
ATpoint
★ 4.6k • written 16 days ago by
mohammedtoufiq91
▴ 10
1
vote
3
replies
355
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 21 days ago by
Melisa Tecik
• 0
0
votes
2
replies
168
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
25 days ago • updated 24 days ago
giulia.gentile
▴ 10
4
votes
2
replies
510
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 25 days ago by
Gordon Smyth
52k • written 25 days ago by
Ahdee
▴ 50
0
votes
2
replies
161
views
Limma Interaction Effect with Covariates
limma
DMRcate
25 days ago
kitzhu
• 0
2
votes
3
replies
866
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 27 days ago by
Gordon Smyth
52k • written 4 weeks ago by
kyj2226
• 0
3
votes
4
replies
602
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
4 weeks ago
dseauer
• 0
1
vote
3
replies
407
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
5 weeks ago • updated 16 days ago
abadgerw
• 0
0
votes
5
replies
596
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
5 weeks ago • updated 11 days ago
abadgerw
• 0
1
vote
8
replies
1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 5 weeks ago by
Adam Marstrand
• 0
1
vote
2
replies
922
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
5 weeks ago
Ai
• 0
3
votes
3
replies
881
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 6 weeks ago by
Satoshi
• 0
4
votes
3
replies
795
views
Analysis of 2*4 factorial design
limma
updated 6 weeks ago by
Gordon Smyth
52k • written 7 weeks ago by
Sudipta
• 0
2
votes
12
replies
1.6k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
7 weeks ago • updated 21 days ago
john
• 0
4
votes
6
replies
1.5k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 7 weeks ago by
Gordon Smyth
52k • written 7 weeks ago by
abadgerw
• 0
4
votes
6
replies
1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
8 weeks ago • updated 6 weeks ago
altintas.ali
• 0
2
votes
2
replies
320
views
Automatically generate contrasts from a model matrix / formula
limma
updated 8 weeks ago by
ATpoint
★ 4.6k • written 8 weeks ago by
Jonathan
▴ 10
3
votes
3
replies
303
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
9 weeks ago • updated 8 weeks ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
344
views
Need help interpreting heatmaps from limma
limma
written 9 weeks ago by
lhwh1208
• 0
2
votes
1
reply
1.4k
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 9 weeks ago by
James W. MacDonald
67k • written 9 weeks ago by
danphillips28
▴ 10
5
votes
4
replies
457
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 9 weeks ago by
ATpoint
★ 4.6k • written 10 weeks ago by
Bioinformagician
• 0
1
vote
2
replies
466
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 10 weeks ago by
Michael Love
43k • written 11 weeks ago by
Ben
▴ 10
0
votes
0
replies
230
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
11 weeks ago • updated 10 weeks ago
tim.meese
• 0
0
votes
2
replies
364
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 10 weeks ago by
Gordon Smyth
52k • written 11 weeks ago by
blmurphy
• 0
0
votes
2
replies
451
views
Question on performing ANOVA-like analysis using limma
limma
updated 12 weeks ago by
Gordon Smyth
52k • written 12 weeks ago by
grubble
• 0
17
votes
9
replies
7.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 12 weeks ago by
James W. MacDonald
67k • written 8.5 years ago by
ompandey
▴ 10
2
votes
1
reply
353
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 3 months ago by
James W. MacDonald
67k • written 3 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
581
views
Unable to install/use limma
limma
Bioconductor
updated 3 months ago by
James W. MacDonald
67k • written 3 months ago by
Jennifer
• 0
3
votes
3
replies
518
views
voom does not seem to properly correct for library size
limma
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
ATpoint
★ 4.6k
1
vote
5
replies
835
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Xuan Yi
• 0
0
votes
3
replies
546
views
Differential expression analysis in time course experiments with DESeq2
DESeq2
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Jay
• 0
3
votes
4
replies
601
views
using limma trend workflow in CAMERA
CAMERA
limma
4 months ago • updated 3 months ago
Jay
• 0
3
votes
3
replies
561
views
One-sided tests with CAMERA-PR
CAMERA
limma
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
Tyler Sagendorf
▴ 10
1
vote
6
replies
702
views
limma and Syntactically Invalid Factor Values
limma
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
571
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
4 months ago
Bioinformagician
• 0
4
votes
3
replies
578
views
Limma comparing gene expression between base line and one treatment
limma
updated 4 months ago by
James W. MacDonald
67k • written 4 months ago by
AL
• 0
0
votes
1
reply
525
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 4 months ago by
ATpoint
★ 4.6k • written 4 months ago by
picasa1983
• 0
2
votes
5
replies
630
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 4 months ago by
James W. MacDonald
67k • written 5 months ago by
sop
• 0
4
votes
14
replies
1.6k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 4 months ago by
Gordon Smyth
52k • written 5 months ago by
Michael E
• 0
3
votes
4
replies
827
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
5 months ago
jcollier
• 0
4
votes
4
replies
1.2k
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
5 months ago
sukeshinik5
▴ 20
0
votes
1
reply
331
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 5 months ago by
James W. MacDonald
67k • written 5 months ago by
Neha
• 0
3
votes
3
replies
510
views
Warning message when running limma with covariates
limma
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
Chris
▴ 20
0
votes
8
replies
1.5k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix
limma
5 months ago
jiachengd
• 0
50 results • Page
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Recent ...
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Answer: Margins for gene_set_enrichment_plot
by
Leonardo Collado Torres
★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction
by
James W. MacDonald
67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library
by
María Calvo
• 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv
by
Guido Hooiveld
★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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