[BioC] Re: Working flow_own CEL file reading problem

[Seth Falcon]

Junshi Yazaki <jyazaki at salk.edu> writes:
> And I shut down my Mac. Is these step correct for making cdf 
> environment? And then I started again.
>
>>  source("http://www.bioconductor.org/getBioC.R")
>>  getBioC()
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

You should only need to run getBioC() once.  This script downloads and
install Bioconductor packages onto your machine.  They'll still be
there when you reboot --- if they are not, you have other problems
(like a missing harddrive ;-)

>>  library(affy)

You will always need to load the packages you will use for each new R
session.

>>Data <- readAffy()
>>eset <- rma(data)

If you wish to work with eset between many sessions, you can use the
save() function to save the result in an R binary file which you can
load again later.  This will be faster than reparsing the original
data.

> I got Error below,
> ***********
> Note: You did not specify a download type.  Using a default value of: Source
> This will be fine for almost all users
>
> Error in getCdfInfo(object) : Could not obtain CDF environment, 
> problems encountered:
> Specified environment specified did not contain arabidopsis_tlgF_4x
> Library - package arabidopsistlgf4xcdf not installed
> Data for package affy did not contain arabidopsis_tlgF_4x
> Bioconductor - arabidopsistlgf4xcdf not available

I think this may be the name mismatch of the files as you noted below.

+ seth