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Limma
•
reset
0
votes
3
replies
1.6k
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP
limma
Bioconductor
ChAMPdata
updated 3 days ago by
81becky
• 0 • written 3.5 years ago by
Jinyue
• 0
1
vote
2
replies
442
views
contrast matrix design for a continuous variable
limma
10 weeks ago • updated 24 days ago
dtzhu337
• 0
2
votes
5
replies
752
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 28 days ago by
James W. MacDonald
68k • written 28 days ago by
Jonathan
▴ 10
2
votes
5
replies
348
views
Differential variability modelling with vst() expression
limma
DESeq2
written 5 weeks ago by
jtsy6383
• 0
0
votes
0
replies
141
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
4 weeks ago
GJ
• 0
0
votes
2
replies
393
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 4 weeks ago by
svlachavas
▴ 840
6
votes
5
replies
597
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 5 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
1sunmic2
• 0
4
votes
4
replies
696
views
Warning message when running limma with covariates
limma
7 months ago • updated 6 weeks ago
Chris
▴ 20
1
vote
9
replies
861
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 8 weeks ago by
anna.cot.anna.cot
▴ 30
0
votes
2
replies
493
views
Cross-validation with multiple control subgroups in limma
limma
multtest
7 weeks ago
Ali Barry
▴ 40
3
votes
3
replies
654
views
Crossover design with limma
limma
crossover
updated 8 weeks ago by
Gordon Smyth
52k • written 11 weeks ago by
Marek Gierlinski
▴ 30
0
votes
2
replies
344
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
9 weeks ago
Tadeoye
▴ 20
6
votes
10
replies
2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 9 weeks ago by
ATpoint
★ 4.7k • written 11 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
508
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 9 weeks ago by
Gordon Smyth
52k • written 10 weeks ago by
Lina
▴ 10
2
votes
3
replies
1.3k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
giulia.gentile
▴ 10
0
votes
9
replies
991
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
abadgerw
• 0
1
vote
3
replies
467
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 11 weeks ago by
Melisa Tecik
• 0
0
votes
5
replies
731
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
3 months ago • updated 10 weeks ago
abadgerw
• 0
1
vote
3
replies
502
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
3 months ago • updated 11 weeks ago
abadgerw
• 0
2
votes
12
replies
1.8k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
3 months ago • updated 11 weeks ago
john
• 0
0
votes
2
replies
230
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
12 weeks ago
giulia.gentile
▴ 10
4
votes
2
replies
622
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 12 weeks ago by
Gordon Smyth
52k • written 12 weeks ago by
Ahdee
▴ 50
1
vote
2
replies
268
views
Limma Interaction Effect with Covariates
limma
DMRcate
12 weeks ago
kitzhu
• 0
2
votes
3
replies
942
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 12 weeks ago by
Gordon Smyth
52k • written 3 months ago by
kyj2226
• 0
8
votes
3
replies
4.3k
views
Appropriate ways to filter counts data for voom/limma
limma
edger
sequencing
written 8.5 years ago by
blofeld
▴ 10
3
votes
4
replies
720
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
3 months ago
dseauer
• 0
1
vote
8
replies
1.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 3 months ago by
Adam Marstrand
• 0
3
votes
3
replies
999
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 3 months ago by
Satoshi
• 0
0
votes
1
reply
669
views
Issue with weights in voomLmFit()
limma
updated 3 months ago by
Gordon Smyth
52k • written 16 months ago by
gabriel.hoffman
▴ 170
1
vote
2
replies
1.0k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
3 months ago
Ai
• 0
4
votes
3
replies
856
views
Analysis of 2*4 factorial design
limma
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Sudipta
• 0
4
votes
6
replies
1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
3 months ago
altintas.ali
• 0
3
votes
2
replies
2.0k
views
Multi-level design RRBS analysis with voomLmFit
edgeR
voomLmFit
limma
duplicateCorrelation
voom
updated 3 months ago by
Gordon Smyth
52k • written 3.2 years ago by
altintas.ali
• 0
7
votes
3
replies
2.2k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
written 14 months ago by
annikagable
• 0
4
votes
6
replies
1.6k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
abadgerw
• 0
0
votes
3
replies
439
views
Need help interpreting heatmaps from limma
limma
written 4 months ago by
lhwh1208
• 0
2
votes
2
replies
433
views
Automatically generate contrasts from a model matrix / formula
limma
updated 4 months ago by
ATpoint
★ 4.7k • written 4 months ago by
Jonathan
▴ 10
34
votes
11
replies
42k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.2 years ago by
Jon Bråte
▴ 260
3
votes
3
replies
377
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
4 months ago
Guido Hooiveld
★ 4.1k
2
votes
1
reply
1.6k
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 4 months ago by
James W. MacDonald
68k • written 4 months ago by
danphillips28
▴ 10
5
votes
4
replies
558
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 4 months ago by
ATpoint
★ 4.7k • written 4 months ago by
Bioinformagician
• 0
0
votes
2
replies
453
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
blmurphy
• 0
1
vote
2
replies
552
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Ben
▴ 10
0
votes
0
replies
274
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
4 months ago
tim.meese
• 0
0
votes
2
replies
528
views
Question on performing ANOVA-like analysis using limma
limma
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
grubble
• 0
17
votes
9
replies
7.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 5 months ago by
James W. MacDonald
68k • written 8.7 years ago by
ompandey
▴ 10
2
votes
1
reply
423
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray
EpigeneticsWorkflow
limma
Regression
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
rae.alshammari
▴ 10
6
votes
6
replies
2.4k
views
limma plotMDS - logFC inverted?
limma
MultidimensionalScaling
updated 5 months ago by
James W. MacDonald
68k • written 2.2 years ago by
Katharina
• 0
0
votes
1
reply
933
views
Unable to install/use limma
limma
Bioconductor
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
Jennifer
• 0
2
votes
5
replies
1.6k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq
limma
edgeR
updated 5 months ago by
Sara
• 0 • written 4.4 years ago by
zliu
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction
by
bbao
▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Votes
Answer: Store Matrix in DataFrame Cell
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
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