DESeq question

[drdna]

I'm trying to load data into R so that I can run DESeq and I am getting the following error:

> datafile = system.file( "PK/extdata/PK_DESeq")
> datafile
[1] ""
> PKCountTable = read.table( datafile, header=TRUE, row.names=1 )
Error in read.table(datafile, header = TRUE, row.names = 1) :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former

R seems to be having a problem finding the file even though it autofills the file path when I use tab. Note that when I retype datafile. It shows an empty path. Anyone have an idea what I am doing wrong?

[Simon Anders]

Any reason why you used the "system.file" function? You did read the explanation in the help page (and the vignette) before asking the question, right?

[drdna]

Thanks for the quick reply Simon. Yes I did read the vignette but it doesn't explain how to load non-example data into R. Unfortunately, I had never used R before so I tried to apply the vignette example to my own situation:

The instructions in the http://bioconductor.org/packages/rel.../doc/DESeq.pdf document only shows how to load the sample data. Specifically, it shows:

> datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )

followed by loading of the "datafile" into the countTable:

> pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 )".

My assumption was that one needed to use the system.file command to define datafile for read.table. However, after looking up various resources for R, I have discovered that one can use the explicit file path for read.table. Once I got that figured out it was very straightforward and I was able to get my first analysis done within 10 minutes. Thanks for an excellent tool.