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SydneyBioX / spicyR

https://sydneybiox.github.io/spicyR/
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vignette unclear #39

Closed SchulzDan closed 9 months ago

SchulzDan commented 9 months ago

Hi,

I am confused with the way that the condition comparisons are performed. In the vignette you use the diabetesData_SCE object and for condition you use the stage entry. However, this entry contains three levels! Which comparison is actually made here?

Many thanks for clarification.

Best, Daniel

alexrunqin commented 9 months ago

Hi Daniel!

Good observation - by default, spicyR uses the first 2 levels of your specified factor column and compares these, with the first level being considered the "base" group. The vignette does not currently cover this, and has now been updated to reflect that.

When actually using the spicy() function there is a warning notification that mentions this, and if you would like to change the conditions being compared, feel free to change the ordering of the levels for your input into the condition = parameter.

Best, Alex