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alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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Math error with logmus of meanmodel #18

Closed warrenmcg closed 9 years ago

warrenmcg commented 9 years ago

Hi Alyssa,

I was excited to try your package after taking Dr. Leek's Coursera series, and finding your work after looking for a way to simulate RNA-Seq data. However, I received an error when I attempted to use simulate_experiment() with meanmodel=TRUE. Digging into the code, I found that the reads_per_transcript parameter had several "Inf" values, which was generated from logmus exponents that were way too high (>1K). Reviewing your document describing where the linear regression came from (http://htmlpreview.github.io/?https://github.com/alyssafrazee/polyester_code/blob/master/length_simulation.html), I saw that the linear regression was of the log2 of the widths of the transcripts, and that this is missing in your original code. Let me know if I modified the code correctly.

Thanks, Warren

alyssafrazee commented 9 years ago

Thanks so much for the fix! Looks great.

warrenmcg commented 9 years ago

You're welcome! :)