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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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basemeans: number of items to replace is not a multiple of replacement length #42

Closed mikelove closed 8 years ago

mikelove commented 8 years ago

The latest commit (also pushed to Bioc devel) produces an error when num_reps has length 2, and fold_changes is a matrix of dimensions: #transcripts x 2. This is the dimension of fold_changes that is specified by the docs:

https://github.com/alyssafrazee/polyester/blob/master/R/simulate_experiment.R#L139-L142

Here's the line that's the problem:

basemeans[,2] = fold_changes * basemeans[,1]

https://github.com/alyssafrazee/polyester/blob/master/R/simulate_experiment.R#L376

Bioc devel build report:

http://bioconductor.org/checkResults/devel/bioc-LATEST/polyester/malbec1-buildsrc.html

(I see you're changing things to support multi-group DE which is great.)

If you're already aware of what's happening feel free to close this issue. If you would like an example and more information, just ping me.

JMF47 commented 8 years ago

Thanks for the headsup, made patching the error much much much easier!

manuelsmendoza commented 5 years ago

is it still bugged?

zhou-ran commented 5 years ago

is it still bugged?