Showing : Limma • reset
0
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5
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8.2k
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Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
written 4.9 years ago by ▴ 10
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
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
12
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5
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5.6k
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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
2
votes
15
replies
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
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7
replies
3.6k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
5
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7
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3.6k
views
limma correction for tumor purity
limma
9 months ago gabriella.jacobson-eisenberg ▴ 20
4
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0
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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
1
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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
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
9
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6
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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
0
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3
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2.4k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
written 22.1 years ago by ▴ 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
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
5
votes
5
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1.9k
views
Limma with covariates
limma
written 20 months ago by ▴ 20
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 • updated 7 months ago Eric • 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
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
2
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2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 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
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
4
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6
replies
1.6k
views
using limma trend workflow in CAMERA
CAMERA limma
updated 7 days ago by 53k • written 18 months ago by • 0
5
votes
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
votes
2
replies
1.6k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 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
2
votes
5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 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 10 months ago by 53k • written 11 months ago by ▴ 10
0
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1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 10 weeks ago by 53k • written 19.0 years ago by ▴ 240
0
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2
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1.3k
views
missing values in limma/contrasts.fit
Microarray limma Regression probe
16.2 years ago • updated 10 weeks ago Gordon Smyth 53k
1
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2
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1.3k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
0
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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
0
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0
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1.1k
views
Re: LIMMA normalizeForPrintorder
BRAIN Normalization limma ASSIGN
22.7 years ago • updated 7 months ago Gordon Smyth 53k
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
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 months ago by • 0
2
votes
8
replies
837
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 6 months ago by ▴ 30
2
votes
1
reply
791
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 months ago by • 0
0
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2
replies
746
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
0
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8
replies
735
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
3
votes
4
replies
662
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
0
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4
replies
657
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
2
votes
2
replies
646
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago sandmann.t ▴ 70
5
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3
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630
views
Limma-voom sample weights and impact on DEG numbers
limma
written 7 weeks ago by ▴ 20
0
votes
0
replies
532
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
9 months ago jamiecatalano2 • 0
0
votes
1
reply
531
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
3
votes
1
reply
525
views
Limpa Pipeline Order
limma limpa
updated 6 months ago by 53k • written 6 months ago by • 0
0
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4
replies
508
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
3
votes
2
replies
507
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
497
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
1
vote
2
replies
447
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
1
vote
3
replies
434
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
56 results • Page 1 of 2
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Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
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 `…
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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