I try to clean data of massarray EpiTYPER using R script provided by GitHub (http://journal.frontiersin.org/article/10.3389/fgene.2015.00287/full). But I am stucking now because of this warning:
> source("C:\\Users\\ Desktop\\EpiTyper-scripts\\ampliconPrediction.R")
> source("C:\\Users\\ Desktop\\EpiTyper-scripts\\ampliconReport.R")
> source("C:\\Users\\ Desktop\\EpiTyper-scripts\\analyzeSequenom.R")
> ampliconReport()
> library(MassArray)
> ASCL169 ampliconPrediction(ASCL169)
> source("C:\\Users\\ Desktop\\EpiTyper-scripts\\Epityper_QC.r")
> directory_name="C://Users//Desktop/EpiTYPER-R"
> setwd=directory_name
> directory=getwd()
> data
Hi,
What are you exactly trying to do? If you have data from Epityper, this is not the way to go to run the script. The quality control on data after you did the Epityper measurements are much easier to do. We have a git hub that explains how to run the QC on data:
https://git.lumc.nl/molepi/EpiTyper/blob/master/Epityper_QC_start.r
If you are still stuck, please let me know. You can directly reach me at r.c.slieker[at]lumc.nl
Cheers,
Roderick
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