Showing : Limma • reset
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396
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Cross-validation with multiple control subgroups in limma
limma multtest
9 days ago • updated 8 days ago Ali Barry ▴ 40
1
vote
9
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722
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 days ago by ▴ 30
0
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2
replies
271
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
20 days ago • updated 19 days ago Tadeoye ▴ 20
0
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2
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447
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 23 days ago by 52k • written 24 days ago by ▴ 10
2
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3
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1.2k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 24 days ago by 67k • written 25 days ago by ▴ 10
1
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2
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306
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contrast matrix design for a continuous variable
limma
27 days ago dtzhu337 • 0
3
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3
replies
588
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Crossover design with limma
limma crossover
updated 13 days ago by 52k • written 4 weeks ago by ▴ 30
0
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9
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839
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 24 days ago by 67k • written 4 weeks ago by • 0
6
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10
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2.5k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 20 days ago by ★ 4.6k • written 4 weeks ago by ▴ 10
1
vote
3
replies
415
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 weeks ago by • 0
0
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2
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191
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 weeks ago giulia.gentile ▴ 10
4
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2
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541
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 5 weeks ago by 52k • written 5 weeks ago by ▴ 50
0
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2
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183
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Limma Interaction Effect with Covariates
limma DMRcate
5 weeks ago kitzhu • 0
2
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3
replies
888
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[How to construct a model.matrix ]
limma modelmatrix
updated 6 weeks ago by 52k • written 6 weeks ago by • 0
3
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4
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640
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
6 weeks ago dseauer • 0
1
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3
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439
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
7 weeks ago • updated 4 weeks ago abadgerw • 0
0
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5
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642
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
7 weeks ago • updated 27 days ago abadgerw • 0
1
vote
8
replies
1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 7 weeks ago by • 0
1
vote
2
replies
947
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
7 weeks ago Ai • 0
3
votes
3
replies
909
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 9 weeks ago by • 0
4
votes
3
replies
809
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Analysis of 2*4 factorial design
limma
updated 8 weeks ago by 52k • written 9 weeks ago by • 0
2
votes
12
replies
1.6k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
9 weeks ago • updated 5 weeks ago john • 0
4
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6
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1.5k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
4
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6
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1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
10 weeks ago • updated 9 weeks ago altintas.ali • 0
2
votes
2
replies
346
views
Automatically generate contrasts from a model matrix / formula
limma
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by ▴ 10
3
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3
replies
320
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
11 weeks ago Guido Hooiveld ★ 4.1k
0
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3
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368
views
Need help interpreting heatmaps from limma
limma
written 11 weeks ago by • 0
2
votes
1
reply
1.4k
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 11 weeks ago by 67k • written 11 weeks ago by ▴ 10
5
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4
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483
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 11 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
1
vote
2
replies
487
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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0
replies
242
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
3 months ago tim.meese • 0
0
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2
replies
394
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
0
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2
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475
views
Question on performing ANOVA-like analysis using limma
limma
updated 3 months ago by 52k • written 3 months ago by • 0
17
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9
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7.1k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 3 months ago by 67k • written 8.6 years ago by ▴ 10
2
votes
1
reply
368
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 3 months ago by 67k • written 3 months ago by ▴ 10
0
votes
1
reply
649
views
Unable to install/use limma
limma Bioconductor
updated 3 months ago by 67k • written 3 months ago by • 0
3
votes
3
replies
543
views
voom does not seem to properly correct for library size
limma
updated 4 months ago by 52k • written 4 months ago by ★ 4.6k
1
vote
5
replies
845
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 months ago by 52k • written 4 months ago by • 0
0
votes
3
replies
569
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 4 months ago by 52k • written 4 months ago by • 0
3
votes
4
replies
633
views
using limma trend workflow in CAMERA
CAMERA limma
4 months ago Jay • 0
3
votes
3
replies
586
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 4 months ago by 52k • written 4 months ago by ▴ 10
1
vote
6
replies
722
views
limma and Syntactically Invalid Factor Values
limma
updated 5 months ago by 52k • written 5 months ago by ★ 1.5k
1
vote
1
reply
594
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
5 months ago Bioinformagician • 0
4
votes
3
replies
598
views
Limma comparing gene expression between base line and one treatment
limma
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
1
reply
556
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
2
votes
5
replies
653
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
4
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14
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1.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 5 months ago by 52k • written 5 months ago by • 0
3
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4
replies
846
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
5 months ago jcollier • 0
4
votes
4
replies
1.2k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
6 months ago sukeshinik5 ▴ 20
0
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1
reply
344
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 6 months ago by 67k • written 6 months ago by • 0
50 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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