[BioC] custom arrays and eventually gcrma

[James W. MacDonald]

Hi Claire,

claire wrote:
> Hello there,
> 
> I am probably doing something really stupid, but I have searched the web and
> the mailing lists and have so far not been able to solve my problem. My
> overall aim is to run gcrma on custom affy arrays. As part of this I have
> been looking at matchprobes and makecdfenv packages. I can successuly use
> make.cdf.env and make.cdf.package. The trouble I am having is in trying to
> install my new CDF package. The output of make.cdf.package is a directory
> which i have then tried to zip up using winzip, in order to use the install
> from local zipped file option. when i do this i get the following error
> message.

Yeah. That won't work.

Here is the message you get from make.cdf.package() in the devel version 
of makecdfenv (suggested by Seth Falcon):

README PLEASE:
A source package has now been produced in
c:/Documents and Settings/Jim/Desktop/CDF and probetabs/cdfs/agcdf.
Before using this package it must be installed via 'R CMD INSTALL'
at a terminal prompt (or DOS command shell).
If you are using Windows, you will need to get set up to install packages.
See the 'R Installation and Administration' manual, specifically
Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset'
for more information.

Alternatively, you could use make.cdf.env(), which will not require you 
to install a package.
However, this environment will only persist for the current R session
unless you save() it.


> 
>>make.cdf.package("XYZ.cdf",species = "Homo_sapiens")
> 
> Creating package in C:/R/custom/xyzcdf
> [1] "xyzcdf"
> 
>>utils:::menuInstallLocal()
> 
> Error in gzfile(file, "r") : unable to open connection
> In addition: Warning messages:
> 1: error -1 in extracting from zip file
> 2: cannot open compressed file 'xyzcdf/DESCRIPTION'
> 
> I was hoping to install the custom cdf as a package so that I could run
> makeProbePackage. When I run makeProbePackage, I get the following error
> 
> XYZ = make.cdf.env("XYZ.cdf")
> makeProbePackage("XYZ",
>                   datafile   = gzfile("XYZ_probes.txt", open="r"),
>                   outdir     = outdir,
>                   maintainer = "me"
>                   version    = "0.0.1",
>                   species    = "Homo_sapiens",
>                   check      = FALSE,
>                   force      = TRUE)
> Importing the data.
> Error in library("xyzcdf") : there is no package called 'xyzcdf'
> Any pointers as to wehre I am going wrong and how i can resolve this would
> be great.

As noted above, you are not installing the cdf package correctly. You 
don't technically need the cdf package to be installed to build the 
probe package. You just need to set the comparewithcdf argument to 
FALSE. However, it is not a bad idea to compare the probe package and 
cdf to make sure things line up correctly.

Best,

Jim


> Many thanks
> 
> claire
> 
>  sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "methods"   "base"
> 
> other attached packages:
> hgu133plus2cdf    matchprobes     simpleaffy     genefilter
> survival     makecdfenv           affy         affyio        Biobase
>       "1.16.0"        "1.8.1"      " 2.10.31"       "1.14.1"
> "2.31"
> "1.14.0"       "1.14.1"        "1.4.0"       "1.14.0"
> 
> 	[[alternative HTML version deleted]]
> 
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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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