When using the the ruProcess() function in the manual analysis pipeline, I would get the following error after an automated run through FIJI:

myobj <- ruProcess(myobj))
#Error in prcomp.default(df, center = T, scale = T) :
#cannot rescale a constant/zero column to unit variance

To solve this, I checked that all channels from my mFISH experiment had non-zero levels of expression. In my 12-probe experiment, my T7 was empty and thus had no signal. Removing the T7 file from the '/NonLinearReg' folder and re-running the RUHi pipeline resolved this issue.

Hey Kaitlin!

The ruCombine() function gives an error when I try to combine 3 data tables all read using the ruRead() function - "Error in UseMethod("mutate"): no applicable method for 'mutate' applied to an object of class "c('double', 'numeric')"

I'm guessing it might have something to do with the metadata columns? I have region, anum, and section filled in for each of the 3 tables.

Screenshot of script + console:

Screenshot of console when I run glimpse(ATN_1)

Thanks sm!! :)