[BioC] Regardin GCRMA normalization

[James W. MacDonald]

Hi Sneha,

sneha patil wrote:
> hii,
> Myself Sneha....
> *I am creating own chip CDF and probe package file with a window R
> *2.0.1
>> * version.
> *>*
> *>* The make.cdf.package works fine,
> *>*
> *make.cdf.package("HuGene-1_0-st-v1.r3.cdf", species = "Homosapiens_sp")
> Reading CDF file.
> Creating CDF environment
> Wait for about 323
> dots..............................................................................................................................................................................................................................................................................................................................
> Creating package in C:/Users/neurooncolab new
> pc/Documents/R/win-library/2.10/hugene10stv1.r3cdf
> 
> README PLEASE:
> A source package has now been produced in
> C:/Users/neurooncolab new
> pc/Documents/R/win-library/2.10/hugene10stv1.r3cdf.
> 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.

Did you read the above message? I tried to make it as explicit as 
possible, but perhaps there is something misleading. If you could tell 
me what exactly you don't understand then I will try to explain it 
further and maybe make changes.

Best,

Jim


> 
>> Rcmd install hugene10stv1.r3cdf
> Error: unexpected symbol in "Rcmd install"
>> R CMD INSTALL hugene10stv1.r3cdf
> Error: unexpected symbol in "R CMD"
>> RCMD INSTALL hugene10stv1.r3cdf
> Error: unexpected symbol in "RCMD INSTALL"
>> hugene10stv1.r3 = make.cdf.env("HuGene-1_0-st-v1.r3.cdf")
> Reading CDF file.
> Creating CDF environment
> Wait for about 323 dots..................>*  *
> 
> **
> *Okkk but now  i am getting the following error *
> **
>> library(hugene10stv1.r3cdf)
> Error in library(hugene10stv1.r3cdf) :
>   'hugene10stv1.r3cdf' is not a valid installed package
> *
> 
> *>* I have tried google, but can not get the right solution. Could any one
> *>* help me to solve the trouble?
> *>* Thanks a lot!
> *
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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