Hi , I have a few questions about use cases for the pigengene package.
For our dataset, I provided both a training dataset and a test dataset, and the one.step.pigengene function did not appear to take the test data into account? The output was exactly the same with or without the test data parameters provided (testD and testLabels). My question is, does the test data have to be same dimension or similar sample size as the training set in order for the function to provide the accuracy of trees on the test data?
If we had already generated our own WGCNA with our own module eigengenes calculated for each sample, could we use that instance instead of running the wgcna.one.step function or the one.step.pigengene function to regenerate a WGCNA instance?
Thank you for your time and help!