Hi all:
I'm new to R and Bioconductor. I'm trying to use makecdfenv package
to
create an environment for tiling arrays on Windows.
This is the error I get:
> make.cdf.package("arabidopsis_tlgF")
Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
Unable to open the file D:/R/rw2001/arabidopsis_tlgF
I previously downloaded Active Perl and MingGW into the above rw2001
directory. What's going on? I'll much appreciate some help.
Ambika Sundaresan.
[[alternative HTML version deleted]]
Hi Ambika,
"Ambika Sundaresan" <sundaresan@salk.edu> writes:
> I'm new to R and Bioconductor. I'm trying to use makecdfenv package
to
> create an environment for tiling arrays on Windows.
>
> This is the error I get:
>
>
>
>> make.cdf.package("arabidopsis_tlgF")
Is there a file in your current working directory with this name?
You can determine your current working directory with getwd() and you
can set it with setwd().
> Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
>
> Unable to open the file D:/R/rw2001/arabidopsis_tlgF
This looks like your working directory is the R install dir. Did you
put data files there? Probably it is a better idea to place them
elsewhere and change your working directory. There is a menu option
for it in the Windows R GUI, but you can also use setwd().
>
> I previously downloaded Active Perl and MingGW into the above rw2001
> directory. What's going on? I'll much appreciate some help.
Putting those packages into the R directory seems strange. You'll
need to give us more details in order to help. But the first thing is
to get your file paths sorted.
Best,
+ seth
Ambika Sundaresan wrote:
> Hi all:
>
>
>
> I'm new to R and Bioconductor. I'm trying to use makecdfenv package
to
> create an environment for tiling arrays on Windows.
>
>
>
> This is the error I get:
>
>
>
>
>>make.cdf.package("arabidopsis_tlgF")
make.cdf.package() expects a .cdf file, and in your call to
make.cdf.package() you should quote the entire filename including the
extension.
make.cdf.package("arabidopsis_tglF.CDF")
Should work, provided this is a CDF file.
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623