R help - May 2008 - A question about *read.table()*

Hi list,

I have a question about using *read.table()* to read in a txt file.
Basically, it
consists of 16346 rows, 6 columns (no header). The code I used is:

exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header
=FALSE)

and I got an error message:
> exprSet <- read.table('process_all4_GSA2.txt', row.names =
1,header
=FALSE)
Error in read.table("process_all4_GSA2.txt", row.names = 1, header =
FALSE)
:
  duplicate 'row.names' are not allowed
In addition: Warning message:
In read.table("process_all4_GSA2.txt", row.names = 1, header = FALSE)
:
  incomplete final line found by readTableHeader on
'process_all4_GSA2.txt'

However, I have no problem with the code to read in a similar txt file which

consists of 22277 rows,  72 columns.
> exprSet <- read.table('70mel_GSA.txt', row.names = 1,header
=FALSE)
> dim(exprSet)
[1] 22277    71
> exprSet[1:4,1:4]
         V2        V3       V4       V5
GENE1  DDR1 10.215229 8.546666 9.207030
GENE2  RFC2  8.028489 8.175520 9.090902
GENE3 HSPA6  4.633769 4.822625 5.125172
GENE4  PAX8  6.121433 6.396281 6.000987

The two txt files are of similar format. The only difference so far I can
tell is that
the second file is of more rows and columns. Other than that, they are
basically
the same. But I don't know what is the issue with the first txt file.

Thank you so much for your help!

Allen

	[[alternative HTML version deleted]]

On May 30, 2008, at 7:56 PM, ss wrote:
> and I got an error message:
>
>> exprSet <- read.table('process_all4_GSA2.txt', row.names =
1,header
> =FALSE)
> Error in read.table("process_all4_GSA2.txt", row.names = 1,
header
> = FALSE)
> :
>   duplicate 'row.names' are not allowed
I would say that's pretty explanatory. You've asked it to use the  
first column for row names, but apparently there are two rows with  
the same name, and we can't have that.
Perhaps you might want to try to load it without the row.names=1  
part, and then use:

duplicated(exprSet[,1])

to see which rows are the ones with the same name.

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College