Entering edit mode
Seth Falcon
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@seth-falcon-992
Last seen 9.6 years ago
Junshi Yazaki <jyazaki@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