I can't tell since you didn't post any code, so forgive me if you've tried this. XLConnect has a colTypes parameter so you could try specifying the relevant columns to be read in as character, set forceConversion = TRUE, and then use as.numeric. Something like this: as.numeric(sub(",", ".", Input, fixed = TRUE)) from http://stackoverflow.com/questions/15236440/as-numeric-with-comma-decimal-separators. That will change the commas to dots and should eliminate the conversion to NA problem you were having.

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