Showing : Limma • reset
2
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[How to construct a model.matrix ]
limma modelmatrix
updated 9 months ago by 52k • written 9 months ago by • 0
3
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4
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1.1k
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
9 months ago dseauer • 0
1
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3
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756
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
9 months ago abadgerw • 0
0
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5
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1.1k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
9 months ago abadgerw • 0
1
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8
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2.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 months ago by • 0
1
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2
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1.3k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
10 months ago Ai • 0
3
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3
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1.4k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 10 months ago by • 0
4
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3
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1.1k
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Analysis of 2*4 factorial design
limma
updated 10 months ago by 52k • written 10 months ago by • 0
2
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12
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2.5k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
10 months ago • updated 9 months ago john • 0
4
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6
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1.8k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 10 months ago by 52k • written 10 months ago by • 0
4
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6
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1.6k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
10 months ago altintas.ali • 0
2
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2
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771
views
Automatically generate contrasts from a model matrix / formula
limma
updated 10 months ago by ★ 4.9k • written 10 months ago by ▴ 10
3
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3
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650
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
10 months ago Guido Hooiveld ★ 4.1k
0
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3
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670
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Need help interpreting heatmaps from limma
limma
written 10 months ago by • 0
2
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1
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1.9k
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 10 months ago by 68k • written 10 months ago by ▴ 10
5
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4
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909
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 10 months ago by ★ 4.9k • written 11 months ago by • 0
1
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2
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788
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 months ago by 43k • written 11 months ago by ▴ 10
0
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0
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426
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
11 months ago tim.meese • 0
0
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2
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709
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
0
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2
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674
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Question on performing ANOVA-like analysis using limma
limma
updated 11 months ago by 52k • written 11 months ago by • 0
17
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9
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8.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 11 months ago by 68k • written 9.3 years ago by ▴ 10
2
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1
reply
639
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 11 months ago by 68k • written 11 months ago by ▴ 20
0
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1
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2.0k
views
Unable to install/use limma
limma Bioconductor
updated 12 months ago by 68k • written 12 months ago by • 0
3
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3
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875
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voom does not seem to properly correct for library size
limma
updated 12 months ago by 52k • written 12 months ago by ★ 4.9k
1
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5
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1.3k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 12 months ago by 52k • written 12 months ago by • 0
0
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3
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843
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 12 months ago by 52k • written 12 months ago by • 0
3
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4
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1.1k
views
using limma trend workflow in CAMERA
CAMERA limma
12 months ago Jiahao Tian • 0
3
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3
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907
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One-sided tests with CAMERA-PR
CAMERA limma
updated 12 months ago by 52k • written 12 months ago by ▴ 10
1
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6
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1.1k
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limma and Syntactically Invalid Factor Values
limma
updated 13 months ago by 52k • written 13 months ago by ★ 1.6k
1
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1
reply
956
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DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
13 months ago Bioinformagician • 0
5
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3
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968
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Limma comparing gene expression between base line and one treatment
limma
updated 13 months ago by 68k • written 13 months ago by • 0
0
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1
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1.1k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
2
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5
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995
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 13 months ago by 68k • written 13 months ago by • 0
4
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14
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2.4k
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LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 13 months ago by 52k • written 13 months ago by • 0
3
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4
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1.2k
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Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
14 months ago • updated 13 months ago jcollier • 0
4
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4
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1.6k
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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
14 months ago sukeshinik5 ▴ 20
0
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1
reply
519
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 14 months ago by 68k • written 14 months ago by • 0
4
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4
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984
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Warning message when running limma with covariates
limma
14 months ago • updated 8 months ago Chris ▴ 20
0
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8
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2.0k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
14 months ago • updated 13 months ago jiachengd • 0
5
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5
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1.6k
views
Limma with covariates
limma
written 14 months ago by ▴ 20
3
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13
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1.8k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 14 months ago by • 0 • written 15 months ago by • 0
3
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2
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1.1k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
15 months ago mohammedtoufiq91 ▴ 10
1
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2
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731
views
Subsetting RNAseq data | voomaByGroup()
limma
15 months ago Anna • 0
1
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2
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953
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
16 months ago Dylan.Sheerin • 0
2
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2
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1.2k
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
16 months ago • updated 15 months ago user_bioinfo • 0
3
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10
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1.7k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 16 months ago by 68k • written 16 months ago by • 0
3
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2
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1.0k
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 15 months ago by 52k • written 16 months ago by • 0
0
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1
reply
648
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 16 months ago by 52k • written 16 months ago by • 0
3
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4
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912
views
Help with error using camera() in limma
CAMERA limma
16 months ago Chris ▴ 20
0
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3
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826
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 16 months ago by 68k • written 16 months ago by • 0
4,221 results • Page 2 of 85
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Replies
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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