Bioconductor Designmatrix

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256

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limma DifferentialExpression Designmatrix

11 days ago Tadeoye ▴ 20

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337

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DESeq2 Designmatrix limma

updated 6 months ago by James W. MacDonald 67k • written 6 months ago by Neha • 0

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588

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subsettingdata edgeR designmatrix

updated 8 months ago by Gordon Smyth 52k • written 8 months ago by prity6459 • 0

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380

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limma designmatrix

updated 8 months ago by Gordon Smyth 52k • written 8 months ago by avery • 0

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1.3k

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DESeq2 designmatrix edgeR limma tidybulk

updated 23 months ago by Michael Love 43k • written 23 months ago by aditya.m ▴ 10

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1.5k

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R designmatrix edgeR limma model.matrix

2.0 years ago Abdul ▴ 20

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1.7k

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DESeq2 limma modelmatrix edgeR designmatrix

updated 3.2 years ago by Gordon Smyth 52k • written 3.2 years ago by rebecca.lea.johnston • 0

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1.4k

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designmatrix deseq2 DESeq2

updated 3.2 years ago by swbarnes2 ★ 1.4k • written 3.2 years ago by OST • 0

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designmatrix RNA-seq limma

updated 3.7 years ago by Gordon Smyth 52k • written 3.7 years ago by athief ▴ 20

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827

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designmatrix DifferentialExpression edgeR RNAseq

3.8 years ago nageshprabhu.k ▴ 10

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1.2k

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MutlipleFactors DesignMatrix edgeR

3.9 years ago Debayan ▴ 20

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1.2k

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edgeR pairedsamples designmatrix

3.9 years ago sfidemw • 0

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915

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deseq2 miRNASeq designmatrix Batch

updated 4.7 years ago by Michael Love 43k • written 4.7 years ago by anshulmbi • 0

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edger r differentialanalysis rnaseq designmatrix

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by Beginner ▴ 60

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Limma designMatrix

updated 6.4 years ago by Aaron Lun ★ 28k • written 6.4 years ago by Keifa ▴ 10

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1.5k

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limma microarray designmatrix

updated 8.4 years ago by Aaron Lun ★ 28k • written 8.4 years ago by nashchem • 0

16 results • Page 1 of 1

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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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