exact counts tables for limma voom guide

Question

[wiscoyogi]

Is there a way to download the exact counts table associated with the limma voom guide? specifically for the tutorial in chapter 15 of the limma voom guide (GSE64099).

I would like to to run through the commands and recreate the plots exactly!

Answer 1

[Gordon Smyth]

The exact counts for the data analyzed in Section 15.6 are available from GEO. The file GSE64099_RAW.tar contains a txt file of counts for each sample, all of which can be read into R using edgeR::readDGE.

Section 15.6 of the limma User's Guide isn't intended to be a full-code case study though, so there will be some filtering and annotation steps not shown. We provide public data and complete end to end code for all the case studies in the limma User's Guide (Chapters 16-18) but not for the earlier chapters, which instead give focus on code for particular analysis steps.