Showing : limma • reset
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107
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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
votes
2
replies
363
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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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97
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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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788
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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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379
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
7 days ago dseauer • 0
0
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1
reply
162
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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
269
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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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962
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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
replies
869
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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
replies
825
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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 1 day ago by 51k • written 26 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 28 days ago by 51k • written 29 days ago by • 0
4
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6
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1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 weeks ago • updated 24 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
3
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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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312
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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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422
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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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208
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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
views
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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421
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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
votes
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
votes
1
reply
446
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
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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
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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556
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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
replies
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
vote
6
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663
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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
vote
1
reply
512
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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
votes
1
reply
446
views
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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592
views
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
votes
4
replies
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
reply
306
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 4 months ago by 67k • written 4 months ago by • 0
3
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3
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472
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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
views
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
views
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
votes
2
replies
622
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
1
vote
2
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447
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Subsetting RNAseq data | voomaByGroup()
limma
6 months ago Anna • 0
1
vote
2
replies
589
views
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
votes
2
replies
673
views
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
replies
991
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
replies
757
views
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
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Answer: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
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
Answer: Differene between the Wald and LRT test for time-series gene expression data by James W. MacDonald 67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
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Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Allele frequencies for ALL alleles of one SNP ?
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Using Affymetrix Custom Array
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