Showing : LIMMA • reset
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109
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
2 days ago • updated 1 day ago giulia.gentile • 0
4
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2
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427
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 2 days ago by 51k • written 2 days ago by ▴ 50
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2
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99
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Limma Interaction Effect with Covariates
limma DMRcate
2 days ago kitzhu • 0
2
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3
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789
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[How to construct a model.matrix ]
limma modelmatrix
updated 4 days ago by 51k • written 7 days ago by • 0
0
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4
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381
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
8 days ago • updated 7 days ago dseauer • 0
0
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1
reply
163
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 days ago • updated 6 days ago abadgerw • 0
0
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1
reply
270
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 days ago • updated 6 days ago abadgerw • 0
1
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8
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963
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 16 days ago by • 0
1
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2
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871
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
16 days ago • updated 15 days ago Ai • 0
3
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3
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826
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 25 days ago by • 0
4
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3
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743
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Analysis of 2*4 factorial design
limma
updated 21 days ago by 51k • written 27 days ago by • 0
2
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12
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1.4k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
updated 2 days ago by 51k • written 27 days ago by • 0
4
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6
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1.4k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 29 days ago by 51k • written 4 weeks ago by • 0
4
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6
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1.0k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 weeks ago • updated 25 days ago altintas.ali • 0
2
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2
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275
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Automatically generate contrasts from a model matrix / formula
limma
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by ▴ 10
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3
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278
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 weeks ago Guido Hooiveld ★ 4.1k
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3
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313
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Need help interpreting heatmaps from limma
limma
written 5 weeks ago by • 0
2
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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 6 weeks ago by 67k • written 6 weeks ago by ▴ 10
5
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4
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423
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
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2
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432
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 8 weeks ago by ▴ 10
0
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0
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210
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
7 weeks ago tim.meese • 0
0
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2
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331
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 weeks ago by 51k • written 8 weeks ago by • 0
0
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2
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422
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Question on performing ANOVA-like analysis using limma
limma
updated 8 weeks ago by 51k • written 8 weeks ago by • 0
17
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9
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7.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 9 weeks ago by 67k • written 8.5 years ago by ▴ 10
2
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1
reply
328
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 9 weeks ago by 67k • written 9 weeks ago by ▴ 10
0
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1
reply
448
views
Unable to install/use limma
limma Bioconductor
updated 11 weeks ago by 67k • written 11 weeks ago by • 0
3
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3
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470
views
voom does not seem to properly correct for library size
limma
updated 12 weeks ago by 51k • written 12 weeks ago by ★ 4.5k
1
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5
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779
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 12 weeks ago by 51k • written 3 months ago by • 0
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3
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513
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 3 months ago by 51k • written 3 months ago by • 0
3
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4
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558
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using limma trend workflow in CAMERA
CAMERA limma
3 months ago • updated 12 weeks ago Jay • 0
3
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3
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522
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One-sided tests with CAMERA-PR
CAMERA limma
updated 3 months ago by 51k • written 3 months ago by ▴ 10
1
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6
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665
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limma and Syntactically Invalid Factor Values
limma
updated 3 months ago by 51k • written 4 months ago by ★ 1.5k
1
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1
reply
513
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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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527
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Limma comparing gene expression between base line and one treatment
limma
updated 4 months ago by 67k • written 4 months ago by • 0
0
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1
reply
451
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 4 months ago by ★ 4.5k • written 4 months ago by • 0
2
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5
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595
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 4 months ago by 67k • written 4 months ago by • 0
4
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14
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1.6k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 3 months ago by 51k • written 4 months ago by • 0
3
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4
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796
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Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
4 months ago jcollier • 0
4
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4
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1.1k
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 • updated 4 months ago sukeshinik5 ▴ 20
0
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1
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307
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 4 months ago by 67k • written 5 months ago by • 0
3
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3
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474
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Warning message when running limma with covariates
limma
updated 5 months ago by 51k • written 5 months ago by ▴ 20
0
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8
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1.5k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
5 months ago • updated 4 months ago jiachengd • 0
5
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4
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661
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Limma with covariates
limma
5 months ago Chris ▴ 20
3
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13
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1.3k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 5 months ago by • 0 • written 5 months ago by • 0
3
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2
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622
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
1
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2
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449
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Subsetting RNAseq data | voomaByGroup()
limma
6 months ago Anna • 0
1
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2
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590
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
6 months ago Dylan.Sheerin • 0
2
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2
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674
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
6 months ago user_bioinfo • 0
3
votes
10
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992
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 6 months ago by 67k • written 6 months ago by • 0
3
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2
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757
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 5 months ago by 51k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Downloading Metagenomic Data with Higher Taxonomic Units by Levi Waldron ★ 1.1k
I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Votes
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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