[BioC] Custom arrays

[James W. MacDonald]

Ho, Anne wrote:
> Hi
> 
> We are working with affy custom arrays. I am trying to create a new
> package for my custom array.
> 
> I was able to create the package using this function: 
> 
>>make.cdf.package("RM-hu0.cdf", species = 'homo_sapiens') 
> 
> Reading CDF file.
> Creating CDF environment
> Wait for about 437
> dots....................................................................
> ........................................................................
> ........................................................................
> ........................................................................
> ........................................................................
> ........................................................................
> ....................
> Creating package in C:/Documents and Settings/Hoa/Desktop/New
> Folder/rmhu01aa520485cdf 
> [1] "rmhu0cdf"
> 
> 
> But I get an error message when I try to install it.
> 2. >C:/PROGRA~1/R/R-2.3.1/bin/RCMD INSTALL rmhu0cdf
> 
> 'make' is not recognized as an internal or external command,
> operable program or batch file.
> *** Installation of rmhu0cdf failed ***
> 
> What should I do? I am using windows XP. 

You have two choices. First, you could use make.cdf.env(), remembering 
to name your env 'RM-hu0cdf' (I think that is correct. if you get an 
error saying it isn't found, the error will say what it is looking for).

Second, you could follow the advice on this page to get set up to build 
packages:

http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

Best,

Jim


> 
> Thanks
> Anne
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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