Showing : limma contrast matrix • reset
3
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Creating a correct limma model with respect to contrast matrix and design matrix
limma limma contrast matrix limma design matrix
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
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4
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Methylation EPIC annotation - the logFC values represented as boxplots
probe to gene id logFC illuminahumanmethylationepicanno.ilm10b2.hg19 limma contrast matrix
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
4
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4
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9.4k
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edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger design and contrast matrix contrast limma contrast matrix limma
updated 7.9 years ago by 53k • written 7.9 years ago by ▴ 20
5
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Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix limma design matrix limma rna-seq limma voom
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
2
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8
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6.5k
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limma interaction contrasts
limma contrast matrix limma design matrix limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 20
2
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15
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4.2k
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limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 10
1
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6
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4.3k
views
Multiple testing limma contrasts
limma limma voom limma contrast matrix multiple testing correction
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 10
3
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5
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2.7k
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Limma-voom contrast confusion
limma limma voom limma design matrix limma contrast matrix limma paired analysis
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
1
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5
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2.4k
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Limma: paired multifactor analysis
limma limma design matrix limma contrast matrix limma paired analysis limma-voom
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 10
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2
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1.2k
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Help with limma contrast/design matrices
limma contrast matrix
9.1 years ago mat149 ▴ 80
0
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4
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1.9k
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contrast matrix design for a comparison (trend) of drug concentrations
limma contrast matrix affymetrix microarrays limma
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 840
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2
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1.8k
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Limma design matrix for three-treatment crossover study
limma design matrix limma limma contrast matrix crossover study
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 10
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Limma contrast for variables disease, gender and age
limma design matrix limma limma contrast matrix microarrays
9.4 years ago miyuki_iii ▴ 10
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limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 9.7 years ago by 53k • written 9.7 years ago by • 0
1
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5
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1.6k
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Question about contrast matrix using limma
limma rna-seq limma contrast matrix
updated 9.7 years ago by 53k • written 9.7 years ago by • 0
2
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4
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10k
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Limma design and contrast matrix
limma limma design matrix limma contrast matrix
9.7 years ago donny.dw • 0
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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