Description Usage Arguments Value Note
This wrapper should probably not be addressed directly except
for debugging. Instead use harman
. Input of PCA scores and the
experiment structure (treatments and batches) and returns a batch corrected
version of the PCA scores matrix
1 2  .callHarman(pc_data_scores, group, limit, numrepeats, randseed, forceRand,
printInfo)

pc_data_scores 
2D NumericMatrix of PCA scores data (from the

group 
The structure of the experiment, consisting of batch numbers and treatment numbers forming 2 rows or columns (HarmanMain works out which). Each entry for a sample describes what batch it came from and what treatment it was given. Has to be integer formated data. 
limit 
A double precsion value indicating the limit of confidence in which to stop removing a batch effect 
numrepeats 
The number of repeats in which to run the simulated batch mean distribution estimator. Probably should be greater than 100,000. 
randseed 
Random seed to pass to the random number generator (0 for use default from system time) 
forceRand 
Force algorithm 
printInfo 
Print update information to screen 
SEXP R list: scores.corrected = harman_res_list["corrected_scores"] correction = harman_res_list["correction"] confidence = harman_res_list["confidence"]
A data matrix with samples in columns must be transposed before PCA analysis and these scores in turn are tweaked a little before handing over to .callHarman. See the example below.
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