Re: Working flow_own CEL file reading problem
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Entering edit mode
Seth Falcon ★ 7.4k
@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
cdf affy cdf affy • 549 views
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