Showing : limma • reset
0
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2
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98
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voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 1 day ago by 43k • written 2 days ago by • 0
0
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1
reply
124
views
limma/voom for protein intensity data
limma proteomics voom
updated 9 days ago by ▴ 840 • written 9 days ago by ▴ 60
3
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5
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343
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How to test full design vs a reduced design in limma?
limma
12 days ago • updated 9 days ago Constantin Ahlmann-Eltze ▴ 10
0
votes
2
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132
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Gene expression in R
limma edgeR Biobase GeneExpression
15 days ago • updated 12 days ago sogol.bouyeh • 0
3
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7
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345
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Nanostringdiff - defining contrast values for blocking variables in glm
limma edgeR DESeq2 NanoStringDiff
updated 12 days ago by 58k • written 19 days ago by • 0
2
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7
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193
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LIMMA - for Microarrays?
limma
written 24 days ago by • 0
1
vote
1
reply
90
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Limma Experimental Design and Contrast Help (Identifying Differentially expressed genes with opposing patterns).
limma DifferentialExpression
updated 26 days ago by 43k • written 26 days ago by • 0
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5
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131
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 28 days ago by 43k • written 28 days ago by • 0
1
vote
1
reply
62
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 28 days ago by 58k • written 28 days ago by • 0
0
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2
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148
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Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP limma Bioconductor ChAMPdata
4 weeks ago • updated 18 days ago Jinyue • 0
3
votes
2
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149
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
5 weeks ago • updated 4 weeks ago Nikshay • 0
1
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2
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133
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Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
5 weeks ago Ahdee ▴ 50
0
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0
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52
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How to handle the imputation and normalisation?
Proteomics DEP limma
6 weeks ago barrypraveen • 0
0
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4
replies
207
views
Batch-corrected expression matrix NOT on a log2 scale
DESeq2 limma
updated 6 weeks ago by 3.4k • written 6 weeks ago by ▴ 60
0
votes
1
reply
121
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question about limma removeBatchEffect and feature selection using elasticnet.
limma
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
4
votes
1
reply
121
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Unit tests for limma package
limma
updated 6 weeks ago by 58k • written 6 weeks ago by • 0
2
votes
2
replies
141
views
plotMDS dimensions bug
limma plotMDS
6 weeks ago jamie.gearing ▴ 50
0
votes
1
reply
87
views
Gene ontology of differentially expressed genes in R
topGO limma DEP
updated 7 weeks ago by 58k • written 7 weeks ago by • 0
0
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1
reply
129
views
Wrong stdev.unscaled from contrasts.fit when lmFit contains a weights matrix
limma
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 10
0
votes
1
reply
151
views
How to extract DEG from limmarResults object after beadarray analysis
beadarray limma
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
1
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2
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195
views
Selecting pairs of exons from differentially spliced genes
diffSplice limma
8 weeks ago • updated 7 weeks ago jamie.gearing ▴ 50
0
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0
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83
views
Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
8 weeks ago edissepo • 0
1
vote
1
reply
128
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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7
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218
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Problems with analysing Agilent G3 GEx Rat V2 chips
Agilent limma
9 weeks ago AB • 0
0
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2
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138
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Help with Limma design matrix
limma R
9 weeks ago • updated 6 weeks ago lintek08 • 0
0
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0
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103
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
10 weeks ago • updated 9 weeks ago barrypraveen • 0
0
votes
1
reply
210
views
Processing Nanostring GeoMX Q3 normalized data as intensities with Limma
Limma GeoMX
updated 5 weeks ago by • 0 • written 11 weeks ago by ▴ 330
2
votes
2
replies
200
views
Questions regard to GSVA and Limma
limma GSVA
12 weeks ago • updated 11 weeks ago Chenxi • 0
1
vote
0
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144
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Normalization of metabolomics/lipidomics data for limma
Lipidomics Metabolomics limma Normalization
12 weeks ago pgugger ▴ 60
0
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4
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201
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
12 weeks ago barrypraveen • 0
1
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3
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206
views
limma - contrast matrix hypothesis testing
limma variancePartition
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
1
vote
2
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155
views
Difference in mixed test for fry vs mroast
limma
updated 3 months ago by 43k • written 3 months ago by 58k
5
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3
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208
views
edgeR calcNormFactors or normalization factors with voom?
edgeR limma
3 months ago XTR5 • 0
2
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2
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184
views
How does the empirical Bayes moderation (eBayes) in the limma pipeline work?
limma
3 months ago Junghoon ▴ 10
0
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1
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178
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 3 months ago by 34k • written 3 months ago by • 0
2
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4
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1.2k
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Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma toptable deg logfc
written 3.0 years ago by • 0
5
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10
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365
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How to do annotation with Limma
annotation limma
updated 3 months ago by ★ 3.0k • written 3 months ago by • 0
2
votes
3
replies
179
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 3 months ago by • 0 • written 3 months ago by • 0
3
votes
4
replies
305
views
Combining repeated measurements and duplicateCorrelation in LIMMA
limma
updated 3 months ago by 58k • written 3 months ago by ▴ 20
3
votes
5
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263
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 11 weeks ago by 43k • written 3 months ago by • 0
0
votes
3
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204
views
[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 3 months ago by 34k • written 3 months ago by ▴ 10
0
votes
0
replies
96
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
3 months ago kyleyxw • 0
0
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0
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105
views
Use limma to a non-genomic data
non-genomic quantitative limma
4 months ago Marcelo Laia ▴ 440
1
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3
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208
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 4 months ago by 43k • written 4 months ago by • 0
2
votes
2
replies
191
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
4 months ago tjbencomo • 0
1
vote
1
reply
211
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4 months ago by 3.4k • written 4 months ago by • 0
0
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0
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107
views
Crossover with repeated measures
limma
4 months ago ijvechetti • 0
1
vote
2
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224
views
limma - removing samples?
ArrayExpress limma arrays
4 months ago RMP87 • 0
0
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3
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231
views
Limma paired analysis design question
limma
updated 4 months ago by 43k • written 4 months ago by ▴ 20
1
vote
0
replies
151
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4 months ago Junghoon ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Per gene Covariates by Michael Love 34k
If you have per gene and per sample corrections, you can use normalization factors (see DESeq2 paper and vignette first on this topic). Fo…
Comment: deseq2 machine sizing best practices for very large data set by Michael Love 34k
I recommend and use limma-voom for large bulk datasets often, it is much faster than GLM-based methods.
Comment: branchpointer: trouble to read gtf by b.signal • 0
Hi Frank, Your example gtf is missing a gene_id. In the old code we also required a transcript_type/transcript_biotype, and a gene_type/g…
Comment: deseq2 machine sizing best practices for very large data set by ATpoint ▴ 840
https://support.bioconductor.org/p/73399/#73400
Comment: Per gene Covariates by Paola • 0
Hi Michael, I have a similar problem where we want to run a LRT analysis on RNA-Seq to find differences across 4 groups and correcting for…
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Answer: Format roxgen comment (alternative to formatR)
Answer: Format roxgen comment (alternative to formatR)
Format roxgen comment (alternative to formatR)
Answer: Format roxgen comment (alternative to formatR)
How does DESeq2 handle zero counts in one condition?
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