Showing : Limma • reset
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196
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 days ago • updated 3 days ago Tadeoye ▴ 20
0
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2
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400
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 7 days ago by 52k • written 8 days ago by ▴ 10
2
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3
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1.1k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 8 days ago by 67k • written 9 days ago by ▴ 10
1
vote
2
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270
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contrast matrix design for a continuous variable
limma
11 days ago dtzhu337 • 0
3
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3
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520
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Crossover design with limma
limma crossover
16 days ago • updated 9 days ago Marek Gierlinski ▴ 30
0
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9
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720
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 8 days ago by 67k • written 14 days ago by • 0
6
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10
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2.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 4 days ago by ★ 4.6k • written 16 days ago by ▴ 10
1
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3
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355
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 21 days ago by • 0
0
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2
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168
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
25 days ago • updated 24 days ago giulia.gentile ▴ 10
4
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2
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510
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 25 days ago by 52k • written 25 days ago by ▴ 50
0
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2
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161
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Limma Interaction Effect with Covariates
limma DMRcate
25 days ago kitzhu • 0
2
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3
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866
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[How to construct a model.matrix ]
limma modelmatrix
updated 27 days ago by 52k • written 4 weeks ago by • 0
3
votes
4
replies
602
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
4 weeks ago dseauer • 0
1
vote
3
replies
407
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 weeks ago • updated 16 days ago abadgerw • 0
0
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5
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596
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 weeks ago • updated 11 days ago abadgerw • 0
1
vote
8
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1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 weeks ago by • 0
1
vote
2
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922
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
5 weeks ago Ai • 0
3
votes
3
replies
881
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 weeks ago by • 0
4
votes
3
replies
795
views
Analysis of 2*4 factorial design
limma
updated 6 weeks ago by 52k • written 7 weeks ago by • 0
2
votes
12
replies
1.6k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
7 weeks ago • updated 21 days ago john • 0
4
votes
6
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1.5k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 7 weeks ago by 52k • written 7 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
8 weeks ago • updated 6 weeks ago altintas.ali • 0
2
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2
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320
views
Automatically generate contrasts from a model matrix / formula
limma
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by ▴ 10
3
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3
replies
303
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
9 weeks ago • updated 8 weeks ago Guido Hooiveld ★ 4.1k
0
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3
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344
views
Need help interpreting heatmaps from limma
limma
written 9 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 9 weeks ago by 67k • written 9 weeks ago by ▴ 10
5
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4
replies
457
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 9 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
1
vote
2
replies
466
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 10 weeks ago by 43k • written 11 weeks ago by ▴ 10
0
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0
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230
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
11 weeks ago • updated 10 weeks ago tim.meese • 0
0
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2
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364
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 10 weeks ago by 52k • written 11 weeks ago by • 0
0
votes
2
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451
views
Question on performing ANOVA-like analysis using limma
limma
updated 12 weeks ago by 52k • written 12 weeks 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 12 weeks ago by 67k • written 8.5 years ago by ▴ 10
2
votes
1
reply
353
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
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1
reply
581
views
Unable to install/use limma
limma Bioconductor
updated 3 months ago by 67k • written 3 months ago by • 0
3
votes
3
replies
518
views
voom does not seem to properly correct for library size
limma
updated 3 months ago by 52k • written 3 months ago by ★ 4.6k
1
vote
5
replies
835
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 3 months ago by 52k • written 3 months ago by • 0
0
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3
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546
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 3 months ago by 52k • written 3 months ago by • 0
3
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4
replies
601
views
using limma trend workflow in CAMERA
CAMERA limma
4 months ago • updated 3 months ago Jay • 0
3
votes
3
replies
561
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
702
views
limma and Syntactically Invalid Factor Values
limma
updated 4 months ago by 52k • written 4 months ago by ★ 1.5k
1
vote
1
reply
571
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
4 months ago Bioinformagician • 0
4
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3
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578
views
Limma comparing gene expression between base line and one treatment
limma
updated 4 months ago by 67k • written 4 months ago by • 0
0
votes
1
reply
525
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
2
votes
5
replies
630
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 4 months ago by 67k • written 5 months ago by • 0
4
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14
replies
1.6k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 4 months ago by 52k • written 5 months ago by • 0
3
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4
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827
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
5 months ago jcollier • 0
4
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4
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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
5 months ago sukeshinik5 ▴ 20
0
votes
1
reply
331
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 5 months ago by 67k • written 5 months ago by • 0
3
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3
replies
510
views
Warning message when running limma with covariates
limma
updated 5 months ago by 52k • written 5 months ago by ▴ 20
0
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8
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1.5k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
5 months ago jiachengd • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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