Bioconductor Multiple comparisons

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1.1k

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deseq2 deseq rna-seq multiple comparisons

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by rbronste ▴ 60

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1.0k

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edger multifactorial design multiple comparisons differential gene expression

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by svlachavas ▴ 840

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1.7k

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deseq2 multiple comparisons contrast

updated 7.0 years ago by James W. MacDonald 67k • written 7.0 years ago by serpalma.v ▴ 60

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2.1k

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deseq2 padj multiple comparisons differential gene expression

updated 7.7 years ago by Michael Love 43k • written 7.7 years ago by tarun2 • 0

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4.7k

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rnaseq multiple comparisons post hoc deseq2

8.6 years ago • updated 7.8 years ago laianavarromartin ▴ 20

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5.6k

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limma design matrix makecontrasts multiple comparisons

7.9 years ago annabelle.congras ▴ 10

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3.3k

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qvalue pvalue r multiple comparisons

updated 7.9 years ago by Storey, John D. ▴ 100 • written 7.9 years ago by tombernardryan ▴ 60

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limma multiple factor design multiple comparisons

updated 8.2 years ago by Gordon Smyth 52k • written 8.2 years ago by xluong • 0

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deseq2 rnaseq contrast multiple comparisons fdrtool

8.6 years ago sebastiano.curreli • 0

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rnaseq pairwise multiple comparisons deseq2

updated 8.8 years ago by Michael Love 43k • written 8.8 years ago by hamaor • 0

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17k

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limma illumina differential gene expression multiple comparisons design matrix

9.6 years ago • updated 9.4 years ago svlachavas ▴ 840

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4.1k

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edger design and contrast matrix multiple factor design multiple comparisons

updated 9.5 years ago by James W. MacDonald 67k • written 9.5 years ago by mouchkam ▴ 20

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3.6k

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deseq2 multiple comparisons

9.5 years ago annalisa.giampetruzzi • 0

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6.2k

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edger multiple comparisons anova glm

updated 9.5 years ago by Ryan C. Thompson ★ 7.9k • written 9.5 years ago by chickenchamp4 ▴ 20

14 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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