Showing : Limma • reset
2
votes
15
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4.5k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma oligo annotation
updated 6 months ago by • 0 • written 11.1 years ago by • 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago • updated 6 months ago bbao ▴ 10
4
votes
8
replies
2.1k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 months ago richardallenfriedmanbrooklyn ▴ 30
2
votes
8
replies
831
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 5 months ago by ▴ 30
0
votes
8
replies
729
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
1
vote
8
replies
2.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 15 months ago by • 0
4
votes
7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
5
votes
7
replies
3.6k
views
limma correction for tumor purity
limma
9 months ago gabriella.jacobson-eisenberg ▴ 20
9
votes
6
replies
2.4k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 11 months ago by • 0 • written 8.1 years ago by ▴ 10
4
votes
6
replies
1.6k
views
using limma trend workflow in CAMERA
CAMERA limma
updated 5 days ago by 53k • written 18 months ago by • 0
12
votes
5
replies
5.5k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
5
votes
5
replies
1.9k
views
Limma with covariates
limma
written 19 months ago by ▴ 20
0
votes
5
replies
8.1k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
written 4.9 years ago by ▴ 10
2
votes
5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 months ago by • 0
0
votes
4
replies
1.9k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
7 months ago Eric • 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 months ago by • 0
3
votes
4
replies
657
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
0
votes
4
replies
503
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 months ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
653
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 5 weeks ago by • 0 • written 7 weeks ago by • 0
1
vote
4
replies
100
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
21 hours ago • updated 27 minutes ago Mariami • 0
2
votes
4
replies
1.7k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
11 months ago svlachavas ▴ 840
5
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
5
votes
3
replies
597
views
Limma-voom sample weights and impact on DEG numbers
limma
written 6 weeks ago by ▴ 20
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
1
vote
3
replies
428
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
0
votes
3
replies
2.4k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
written 22.1 years ago by ▴ 70
0
votes
3
replies
1.2k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 10 months ago by ▴ 10
0
votes
3
replies
2.6k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 7 months ago by 53k • written 7 months ago by • 0
1
vote
2
replies
1.2k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
0
votes
2
replies
1.3k
views
missing values in limma/contrasts.fit
Microarray limma Regression probe
16.2 years ago • updated 10 weeks ago Gordon Smyth 53k
0
votes
2
replies
1.7k
views
how does limma calculate the coefficients with using different design matrix?
probe limma
15.5 years ago • updated 10 weeks ago Gordon Smyth 53k
3
votes
2
replies
6.5k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago Geoff • 0
2
votes
2
replies
641
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago sandmann.t ▴ 70
2
votes
2
replies
492
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 0
0
votes
2
replies
357
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
4 weeks ago • updated 19 days ago Andrew Pattison • 0
4
votes
2
replies
366
views
When to use edgeR or limma
edgeR limma
updated 24 days ago by 53k • written 27 days ago by • 0
0
votes
2
replies
1.5k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
738
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
1
vote
2
replies
444
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
1
vote
2
replies
418
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
2
votes
2
replies
337
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 weeks ago • updated 11 weeks ago jamie.gearing ▴ 60
3
votes
2
replies
505
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by 53k • written 6 months ago by ▴ 20
2
votes
2
replies
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
1
reply
1.5k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 7 months ago by 53k • written 17.0 years ago by ▴ 10
1
vote
1
reply
1.1k
views
ordinary t from limma [was: How would I normally compare swirl?]
GO limma Bioconductor
21.7 years ago • updated 4 months ago Gordon Smyth 53k
0
votes
1
reply
273
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 10 weeks ago by 53k • written 18.9 years ago by ▴ 240
56 results • Page 1 of 2
Recent ...
Replies
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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