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I read in your call to the transformData() function that the decidedTransformList object was not found. This usually means that the parametersTransformation.rds file exported by the Shiny app in the output > 1_Transformation directory is absent. Is it the case for you?
Did you actually exported the transformation parameters generated with the previous Shiny app function (launchTransformationTuninShinyApp()) through the Export button before closing it?
I am testing out PICAFlow with the sample dataset from the tutorial and keep running into this error after the transformation step.
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