Showing : Limma • reset
1
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4
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280
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
4 days ago • updated 3 days ago Mariami • 0
4
votes
2
replies
407
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When to use edgeR or limma
edgeR limma
updated 28 days ago by 53k • written 4 weeks ago by • 0
0
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2
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393
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
5 weeks ago • updated 22 days ago Andrew Pattison • 0
5
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3
replies
643
views
Limma-voom sample weights and impact on DEG numbers
limma
written 7 weeks ago by ▴ 20
0
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4
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662
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How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 5 weeks ago by • 0 • written 8 weeks ago by • 0
2
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2
replies
348
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 weeks ago jamie.gearing ▴ 60
0
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1
reply
283
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
5
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13
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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
0
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4
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510
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
1
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3
replies
438
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
3
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4
replies
665
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 5 months ago by • 0 • written 6 months ago by • 0
2
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8
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840
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 6 months ago by ▴ 30
1
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2
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424
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
1
vote
2
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449
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
529
views
Limpa Pipeline Order
limma limpa
updated 6 months ago by 53k • written 6 months ago by • 0
3
votes
2
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508
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
0
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8
replies
740
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
2
votes
2
replies
501
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
651
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago sandmann.t ▴ 70
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
7
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9
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5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
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3
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2.6k
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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
0
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4
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1.9k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
8 months ago Eric • 0
3
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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
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3
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1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
0
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1
reply
531
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
0
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2
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1.6k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 9 months ago by • 0
0
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2
replies
749
views
Limma suqeezeVar
limma
9 months ago • updated 8 months ago Mengchun • 0
2
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5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 months ago by • 0
5
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7
replies
3.6k
views
limma correction for tumor purity
limma
9 months ago gabriella.jacobson-eisenberg ▴ 20
4
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7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
0
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0
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534
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
9 months ago jamiecatalano2 • 0
2
votes
1
reply
792
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 months ago by • 0
2
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4
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2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 months ago by • 0 • written 10 months ago by • 0
0
votes
3
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1.2k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
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
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 months ago by • 0
5
votes
3
replies
1.4k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 11 months ago by 53k • written 11 months ago by ▴ 10
2
votes
2
replies
1.8k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 0
1
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2
replies
1.3k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
2
votes
4
replies
1.8k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
11 months ago svlachavas ▴ 840
1
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8
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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
6
replies
1.7k
views
using limma trend workflow in CAMERA
CAMERA limma
updated 9 days ago by 53k • written 18 months ago by • 0
5
votes
5
replies
1.9k
views
Limma with covariates
limma
written 20 months ago by ▴ 20
12
votes
5
replies
5.6k
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
0
votes
5
replies
8.2k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
written 4.9 years ago by ▴ 10
9
votes
6
replies
2.4k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 11 months ago by • 0 • written 8.2 years ago by ▴ 10
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
4
votes
0
replies
3.5k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray Normalization Bayesian Regression Cancer limma Microarray Normalization Cancer
updated 9 months ago by • 0 • written 14.7 years ago by ★ 2.0k
0
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2
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1.7k
views
how does limma calculate the coefficients with using different design matrix?
probe limma
15.5 years ago • updated 11 weeks ago Gordon Smyth 53k
56 results • Page 1 of 2
Recent ...
Replies
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
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