Bioconductor Gene set testing

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760

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mroast camera gene set testing

4.2 years ago svlachavas ▴ 840

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2.5k

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limma camera gene set testing ensembl

updated 5.0 years ago by Robert Castelo ★ 3.4k • written 5.0 years ago by Jeremy Beales ▴ 10

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limma agilent microarrays mroast fry gene tests gene set testing

updated 6.2 years ago by Gordon Smyth 52k • written 6.2 years ago by svlachavas ▴ 840

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1.7k

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limma camera cameraPR edgeR gene set testing

updated 6.3 years ago by Gordon Smyth 52k • written 6.3 years ago by jamie.gearing ▴ 60

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1.4k

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limma roast statistics source code gene set testing

6.3 years ago Andrea Carenzo • 0

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gage gene set testing

updated 6.6 years ago by Luo Weijun ★ 1.6k • written 6.6 years ago by Aurora ▴ 20

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EGSEA gene set testing vooma limma voom gsea

updated 7 months ago by Chris ▴ 20 • written 8.0 years ago by Pekka Kohonen ▴ 190

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limma agilent microarrays gene set testing annotation

7.9 years ago Bouzid.a ▴ 20

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8.1 years ago Jon Bråte ▴ 260

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1.8k

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gene set testing camera edger

updated 8.5 years ago by Gordon Smyth 52k • written 8.5 years ago by le2336 ▴ 20

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gsea ncrna coexpression gene set analysis gene set testing

8.7 years ago m.fletcher ▴ 20

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limma camera gene set testing

8.7 years ago claire.n.levy ▴ 10

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3.4k

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limma mroast barcodeplot KEGG gene set testing

updated 9.1 years ago by Gordon Smyth 52k • written 9.1 years ago by svlachavas ▴ 840

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2.1k

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gene set testing roast mroast differential gene expression bioconductor

9.6 years ago svlachavas ▴ 840

14 results • Page 1 of 1

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

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…

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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