Contradictory output RStudio vs R Interface

Hi, I am using qmethod library. Using the same data set and same commands I noticed the output generates differently when I run the interface. i.e general stats are significantly different in relation to some factors. I also noticed factor scores (Results$zsc_n) output contains a mistake. How should I deal with this conflict? Which platform is more reliable?

I would try restarting RStudio. Actually a complete system reboot might be a good idea.

For us to check things out we will need a reproducible example (reprex)

Preferably with all your data or a sample of it that illustrates the problem. A handy way to supply sample data is to use the dput() function. See ?dput. If you have a very large data set then something like head(dput(myfile), 100) will likely supply enough data for us to work with.

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