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bcbio / bcbioR

R package with well defined templates for most common pipelines
https://bcbio.github.io/bcbioR/
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RNA-DE numerator and denominator #54

Closed eberdan closed 1 week ago

eberdan commented 1 week ago

In the params section both are preceded by a # which makes the user ignore them but they need to be set to load the data.

eberdan commented 1 week ago

Additionally, I had to manually call them to get the load function to work:

numerator=params$numerator
denominator=params$denominator

These commands are present in the template but commented out as well.

lpantano commented 1 week ago

we are using list in the contrast variable to allow for multiple comparisons:

contrasts=list(c("sample_type", "tumor", "normal"))