Showing : Limma • reset
2
votes
8
replies
368
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
written 16 days ago by ▴ 30
3
votes
3
replies
214
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 14 days ago by 52k • written 15 days ago by • 0
1
vote
1
reply
114
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 19 days ago by 52k • written 19 days ago by ▴ 10
1
vote
2
replies
186
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
23 days ago • updated 21 days ago richardallenfriedmanbrooklyn ▴ 30
2
votes
1
reply
187
views
Limpa Pipeline Order
limma limpa
updated 26 days ago by 52k • written 26 days ago by • 0
2
votes
2
replies
244
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 25 days ago by 52k • written 28 days ago by ▴ 10
0
votes
8
replies
431
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
28 days ago • updated 24 days ago Jiahao Tian • 0
2
votes
2
replies
247
views
Limma : paired samples leading to unexpected estimates
limma
4 weeks ago Basti ▴ 780
2
votes
2
replies
268
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
4 weeks ago sandmann.t ▴ 70
4
votes
8
replies
1.7k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 weeks ago • updated 6 weeks ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.3k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 weeks ago • updated 6 weeks ago bbao ▴ 10
0
votes
1
reply
1.2k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 7 weeks ago by 52k • written 16.6 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
0
votes
4
replies
1.6k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
10 weeks ago Eric • 0
3
votes
2
replies
6.2k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
3 months ago Geoff • 0
2
votes
3
replies
1.2k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
3 months ago Paulito • 0
0
votes
1
reply
393
views
Typo in the help of lmFit()
limma
updated 3 months ago by 52k • written 3 months ago by • 0
0
votes
2
replies
599
views
Limma suqeezeVar
limma
3 months ago Mengchun • 0
0
votes
2
replies
549
views
Limma trend with limpa
limpa limma trend
updated 3 months ago by 52k • written 3 months ago by • 0
2
votes
5
replies
1.1k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 3 months ago by • 0
5
votes
7
replies
3.2k
views
limma correction for tumor purity
limma
3 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
872
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 4 months ago by ▴ 10
2
votes
6
replies
2.9k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
4 months ago • updated 3 months ago massimo • 0
0
votes
0
replies
383
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
4 months ago jamiecatalano2 • 0
2
votes
1
reply
624
views
ROAST for small sets
limma mroast
updated 4 months ago by 52k • written 4 months ago by • 0
2
votes
4
replies
1.7k
views
how to use `arrayWeightsQuick()`?
limma
updated 3 months ago by • 0 • written 4 months ago by • 0
2
votes
2
replies
1.4k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
2
votes
3
replies
866
views
Explanation for ROAST results
CAMERA limma
updated 5 months ago by 52k • written 5 months ago by • 0
5
votes
3
replies
1.1k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 5 months ago by 52k • written 5 months ago by ▴ 10
2
votes
2
replies
1.4k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
5 months ago Elizabeth • 0
1
vote
2
replies
988
views
Differential expression of proteins using somascan data
somascan limma
written 5 months ago by • 0
2
votes
4
replies
1.3k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
6 months ago svlachavas ▴ 840
3
votes
5
replies
1.8k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 7 months ago by 68k • written 7 months ago by ▴ 10
0
votes
0
replies
316
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
7 months ago GJ • 0
0
votes
2
replies
600
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 7 months ago by ▴ 840
2
votes
5
replies
687
views
Differential variability modelling with vst() expression
limma DESeq2
written 7 months ago by • 0
6
votes
5
replies
953
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 months ago by 68k • written 8 months ago by • 0
0
votes
2
replies
712
views
Cross-validation with multiple control subgroups in limma
limma multtest
8 months ago Ali Barry ▴ 40
1
vote
9
replies
1.3k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 8 months ago by ▴ 30
0
votes
2
replies
588
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
8 months ago Tadeoye ▴ 20
0
votes
2
replies
791
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 8 months ago by 52k • written 8 months ago by ▴ 10
2
votes
3
replies
1.6k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 9 months ago by 68k • written 9 months ago by ▴ 10
1
vote
2
replies
644
views
contrast matrix design for a continuous variable
limma
9 months ago • updated 7 months ago dtzhu337 • 0
3
votes
3
replies
941
views
Crossover design with limma
limma crossover
updated 8 months ago by 52k • written 9 months ago by ▴ 30
0
votes
9
replies
1.5k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 9 months ago by 68k • written 9 months ago by • 0
6
votes
10
replies
3.2k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 8 months ago by ★ 4.9k • written 9 months ago by ▴ 10
1
vote
3
replies
697
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 9 months ago by • 0
0
votes
2
replies
374
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
9 months ago giulia.gentile ▴ 10
4
votes
2
replies
1.1k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 9 months ago by 52k • written 9 months ago by ▴ 60
1
vote
2
replies
463
views
Limma Interaction Effect with Covariates
limma DMRcate
9 months ago kitzhu • 0
4,221 results • Page 1 of 85
Recent ...
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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