Thanks again for your quick reply. I understood your procedure but now it is even more strange why my conversion does not work. In your example, the NA values are in "brackets" <NA> and what your procedure does is to convert these <NA> values into NA and then it seems to be possible to use data.matrix to correctly convert the data.frame into a data.matrix. But the data I read into R are already in that form that the NA values are displayed as NA rather than <NA>. So the conversion should actually work.
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