[BioC] Working flow_own CEL file reading problem

[Junshi Yazaki]

Hi Jim,

Thank you very  much for your suggestion.
I tried make environment again like attached txt as you said.

>>>source("http://www.bioconductor.org/getBioC.R")
>>>getBioC("all")
>>>library(makecdfenv)
>>>Library(affy)
>>>make.cdf.package ("arabidopsistlgF.cdf")
>>
>>And move to Terminal on my Mac,
>>
>>>R CMD INSTALL arabidopsistlgfcdf

back to R

>>>  source("http://www.bioconductor.org/getBioC.R")
>>>  getBioC()
>>>  library(affy)
>>>Data <- readAffy()
>
>  >cleancdfname(cdfName(Data))
>[1] "arabidopsistlgf4xcdf"
>  > cleancdfname("arabidopsistlgf4xcdf")
>[1] "arabidopsistlgf4xcdfcdf"
>  > library(makecdfenv)
>  >make.cdf.package("arabidopsistlgF.cdf", packagename="arabidopsistlgf4xcdf")
>Reading CDF file.
>Creating CDF environment
>Wait for about 0 dots
>>  cel.files=list.files(pattern=".CEL$")
>>  data=ReadAffy(filenames=cel.files)
>>  eset <- rma(Data)
>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 command "make.cdf.package("arabidopsistlgF.cdf", 
packagename="arabidopsistlgf4xcdf")" does work.
But according to above message, I can not make cdf environment 
(Bioconductor - arabidopsistlgf4xcdf not available). Could you please 
help me what should I do more?

Thank you,
Junshi
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Junshi Yazaki, Ph D

The Salk Institute for Biological Studies

10010 North Torrey Pines Road
La  Jolla, CA 92037
Phone (858) 453-4100 x1533
FAX (858) 558-6379
Email: jyazaki at salk.edu

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