It would appear that your file is not a csv file, but we cannot tell for sure 
without seeing an example of the data that you are reading in, can you cut and 
paste the first few lines of the file? Or post a link to a copy of the file.  
If the data is not able to be shared, then create a new (small) file with made 
up data that displays the same problems (creating the example sometimes helps 
you fix the problem yourself) then share that file.

Also why are you specifying sep="," in read.csv? that is a bit redundant.

-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of bonnieyuan
Sent: Tuesday, September 13, 2011 10:09 AM
To: r-help@r-project.org
Subject: [R] import csv file into R, strange problem

Hi, I used read.csv(file name, header=T, sep=",") to bring in a csv file I
saved in MS Excel. The strange thing is all the data ended up in one big
column. The number of rows match with the number of observations, but all
the variables got squeezed into one column. Also the first row where the
header is, the variables names have a dot between them, replacing the comma
that's in the original csv file. 

What did I do wrong here?

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