*cuff-UDPATED.rda files missing

leekgroup / derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data

http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short?rss=1

MIT License

22 stars 11 forks source link

*cuff-UDPATED.rda files missing #13

Closed brianhigh closed 9 years ago

brianhigh commented 9 years ago

When trying to run analysis_code.R, the "chunk 3a: load resuls from Cufflinks" section gives missing file errors because the *cuff-UDPATED.rda files are missing:

https://github.com/alyssafrazee/derfinder/search?utf8=%E2%9C%93&q=cuff-updated

I do not see where in this script the files are saved, nor do I see another script that saves these. Please help me understand where and how these files should have been saved. Thanks!

alyssafrazee commented 9 years ago

These files were created by running Cufflinks/Cuffmerge/Cuffdiff (version 2.0.0) on the bam files in "data". I've uploaded them to the repository so they can be loaded.

As soon as I have a chance, I will address the other issues you opened this weekend. (This upcoming week is extremely busy for me, so it may take some time.)

brianhigh commented 9 years ago

Thanks, Alyssa! It would really be great to be able to reproduce your analysis.