This question is unanswerable as asked. It's like asking 'How do I drive a car?', and the answer is 'Uh, by getting in and driving it?'.

If you have a specific question, and have some code that you have tried, then maybe somebody could help you. But asking non-specific, open-ended questions won't generate much enthusiasm to help you.

Please don't answer your own question with a comment (the box below, labeled 'Add your answer' is for adding answers, not additional comments. Use 'ADD COMMENT' for that).

Your question has nothing to do with any Bioconductor packages, and instead is a basic question about importing data into R. You could just google that error to get (does a quick google search) 3,930 responses to people asking about that exact error message. That's what you should almost always do first. Learning to help yourself will get you farther faster than asking people on a message board.

In future, you should post questions about basic R stuff to r-help@r-project.org, but AFTER you have tried googling for solutions.

That said, are you trying to read an Excel worksheet? You can't use read.table to read an XML document - you need one of the CRAN packages designed for that, like openxlsx etc.

> read.table("Book1.xlsx")
              V1
1 PK\003\004\024
Warning messages:
1: In read.table("Book1.xlsx") : line 1 appears to contain embedded nulls
2: In read.table("Book1.xlsx") :
  incomplete final line found by readTableHeader on 'Book1.xlsx'