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limma
•
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0
votes
0
replies
10
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
3 hours ago
massimo
• 0
0
votes
0
replies
53
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
22 hours ago
jamiecatalano2
• 0
2
votes
1
reply
385
views
ROAST for small sets
limma
mroast
updated 4 days ago by
Gordon Smyth
52k • written 5 days ago by
Jay
• 0
2
votes
3
replies
1.4k
views
how to use `arrayWeightsQuick()`?
limma
updated 16 days ago by
Gordon Smyth
52k • written 17 days ago by
matthew
• 0
0
votes
2
replies
476
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
updated 14 days ago by
Gordon Smyth
52k • written 19 days ago by
skiaphrene
▴ 10
2
votes
2
replies
1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 4 weeks ago by
ATpoint
★ 4.8k • written 4 weeks ago by
robinpaul85
• 0
2
votes
3
replies
698
views
Explanation for ROAST results
CAMERA
limma
updated 4 weeks ago by
Gordon Smyth
52k • written 4 weeks ago by
Jay
• 0
5
votes
3
replies
838
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 5 weeks ago by
Gordon Smyth
52k • written 5 weeks ago by
Devin
▴ 10
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
6 weeks ago • updated 5 weeks ago
Elizabeth
• 0
1
vote
2
replies
844
views
Differential expression of proteins using somascan data
somascan
limma
written 7 weeks ago by
kkeole1
• 0
2
votes
4
replies
990
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
9 weeks ago • updated 7 weeks ago
svlachavas
▴ 840
3
votes
5
replies
1.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Jonathan
▴ 10
0
votes
0
replies
206
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
3 months ago
GJ
• 0
0
votes
2
replies
499
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 3 months ago by
svlachavas
▴ 840
2
votes
5
replies
519
views
Differential variability modelling with vst() expression
limma
DESeq2
written 3 months ago by
jtsy6383
• 0
6
votes
5
replies
763
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
1sunmic2
• 0
0
votes
2
replies
576
views
Cross-validation with multiple control subgroups in limma
limma
multtest
4 months ago
Ali Barry
▴ 40
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 4 months ago by
anna.cot.anna.cot
▴ 30
0
votes
2
replies
437
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
4 months ago
Tadeoye
▴ 20
0
votes
2
replies
619
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
Lina
▴ 10
2
votes
3
replies
1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
giulia.gentile
▴ 10
1
vote
2
replies
532
views
contrast matrix design for a continuous variable
limma
4 months ago • updated 3 months ago
dtzhu337
• 0
3
votes
3
replies
798
views
Crossover design with limma
limma
crossover
updated 4 months ago by
Gordon Smyth
52k • written 5 months ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
1.2k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
abadgerw
• 0
6
votes
10
replies
2.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 4 months ago by
ATpoint
★ 4.8k • written 5 months ago by
mohammedtoufiq91
▴ 10
1
vote
3
replies
571
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by
Melisa Tecik
• 0
0
votes
2
replies
294
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 months ago
giulia.gentile
▴ 10
4
votes
2
replies
769
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
Ahdee
▴ 60
1
vote
2
replies
353
views
Limma Interaction Effect with Covariates
limma
DMRcate
5 months ago
kitzhu
• 0
2
votes
3
replies
1.1k
views
[How to construct a model.matrix ]
limma
modelmatrix
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
kyj2226
• 0
3
votes
4
replies
895
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
5 months ago
dseauer
• 0
1
vote
3
replies
598
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
5 months ago
abadgerw
• 0
0
votes
5
replies
888
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
5 months ago • updated 4 months ago
abadgerw
• 0
1
vote
8
replies
1.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 5 months ago by
Adam Marstrand
• 0
1
vote
2
replies
1.1k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
5 months ago
Ai
• 0
3
votes
3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 6 months ago by
Satoshi
• 0
4
votes
3
replies
975
views
Analysis of 2*4 factorial design
limma
updated 5 months ago by
Gordon Smyth
52k • written 6 months ago by
Sudipta
• 0
2
votes
12
replies
2.2k
views
limma technical repeat correction
limma
lmer
duplicateCorrelation
technicalrepeats
6 months ago • updated 5 months ago
john
• 0
4
votes
6
replies
1.7k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 6 months ago by
Gordon Smyth
52k • written 6 months ago by
abadgerw
• 0
4
votes
6
replies
1.5k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma
duplicateCorrelation
edgeR
modelMatrixMeth
voomLmFit
6 months ago
altintas.ali
• 0
2
votes
2
replies
579
views
Automatically generate contrasts from a model matrix / formula
limma
updated 6 months ago by
ATpoint
★ 4.8k • written 6 months ago by
Jonathan
▴ 10
3
votes
3
replies
482
views
How to subset voomLmFit (MArrayLM) object?
limma
edgeR
6 months ago
Guido Hooiveld
★ 4.1k
0
votes
3
replies
574
views
Need help interpreting heatmaps from limma
limma
written 6 months ago by
lhwh1208
• 0
2
votes
1
reply
1.8k
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 6 months ago by
James W. MacDonald
68k • written 6 months ago by
danphillips28
▴ 10
5
votes
4
replies
743
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 6 months ago by
ATpoint
★ 4.8k • written 6 months ago by
Bioinformagician
• 0
1
vote
2
replies
655
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 7 months ago by
Michael Love
43k • written 7 months ago by
Ben
▴ 10
0
votes
0
replies
345
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
7 months ago
tim.meese
• 0
0
votes
2
replies
569
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 6 months ago by
Gordon Smyth
52k • written 7 months ago by
blmurphy
• 0
0
votes
2
replies
625
views
Question on performing ANOVA-like analysis using limma
limma
updated 7 months ago by
Gordon Smyth
52k • written 7 months ago by
grubble
• 0
17
votes
9
replies
7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7 months ago by
James W. MacDonald
68k • written 8.9 years ago by
ompandey
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Intepretation of results
by
Tom
• 0
[Locksmith Wombwell][1] I have been interested in using AUCell as a way to determine significantly enriched pathways in my single cell spat…
Comment: Gene Ontology (GO) Analysis
by
Tom
• 0
[Locksmith near me][1] Hello, I'm learning about Gene Ontology analysis. I'm trying to understand the difference between the hyperGTest fun…
Comment: DiffBind; Error: No sites have activity greater than filter value
by
etiennedanis
• 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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