Question

CDf files in R

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ekl • 0

@ekl-22229

Last seen 5.0 years ago

i am trying to load a CDf file into R so that Affy can read it along with a cel file. The CDF file is connected to the data in the CEL file. How do I get affy to read a CDf file? Thank you. The code that I am getting is below.

 eset<-ReadAffy(celfile.path="C:\\Users\\EKL\\Downloads\\GSE57629_RAW")
> eset<-ReadAffy(cdffile.path="C:\\Users\\EKL\\Downloads\\GPL8345_AFLAVUSa520391F.cdf")
Error: the following are not valid files:
    C:\Users\EKL\Downloads\GPL8345_AFLAVUSa520391F.cdf
> eset<-ReadAffy(cdffile.path="C:\Users\EKL\Downloads\GPL8345_AFLAVUSa520391F.cdf)
Error: '\U' used without hex digits in character string starting ""C:\U"
> eset<-ReadAffy(cdffile.path="C:\\Users\\EKL\\Downloads\\GPL8345_AFLAVUSa520391F.cdf")
Error: the following are not valid files:
    C:\Users\EKL\Downloads\GPL8345_AFLAVUSa520391F.cdf
>

affy CDF • 2.1k views

ADD COMMENT • link updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by ekl • 0

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This is what I got after doing what you suggested.

The downloaded binary packages are in C:\Users\EKL\AppData\Local\Temp\RtmpE9Qnca\downloadedpackages Old packages: 'BiocManager', 'boot', 'digest', 'foreign', 'hms', 'KernSmooth', 'mgcv', 'nlme', 'rlang' Update all/some/none? [a/s/n]: library(makecdfenv) Update all/some/none? [a/s/n]: make.cdf.package("C:\Users\EKL\Downloads\GPL8345AFLAVUSa520391F.cdf", "aflavusa520391fcdf", version = "0.0.1", species = "Aspergillus_flavus") Update all/some/none? [a/s/n]: install.packages("aflavus520391fcdf", type = "source", repos = NULL) Update all/some/none? [a/s/n]: n

library(affy) eset<-ReadAffy(celfile.path="C:\Users\EKL\Downloads\GSE57629_RAW") eset AffyBatch object size of arrays=716x716 features (26 kb) cdf=AFLAVUSa520391F (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain AFLAVUSa520391F Library - package aflavusa520391fcdf not installed Bioconductor - aflavusa520391fcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)

ADD REPLY • link 5.1 years ago ekl • 0

0

Entering edit mode

This is what I got after doing what you suggested.

The downloaded binary packages are in C:\Users\EKL\AppData\Local\Temp\RtmpE9Qnca\downloadedpackages Old packages: 'BiocManager', 'boot', 'digest', 'foreign', 'hms', 'KernSmooth', 'mgcv', 'nlme', 'rlang' Update all/some/none? [a/s/n]: library(makecdfenv) Update all/some/none? [a/s/n]: make.cdf.package("C:\Users\EKL\Downloads\GPL8345AFLAVUSa520391F.cdf", "aflavusa520391fcdf", version = "0.0.1", species = "Aspergillus_flavus") Update all/some/none? [a/s/n]: install.packages("aflavus520391fcdf", type = "source", repos = NULL) Update all/some/none? [a/s/n]: n

library(affy) eset<-ReadAffy(celfile.path="C:\Users\EKL\Downloads\GSE57629_RAW") eset AffyBatch object size of arrays=716x716 features (26 kb) cdf=AFLAVUSa520391F (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain AFLAVUSa520391F Library - package aflavusa520391fcdf not installed Bioconductor - aflavusa520391fcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)

ADD REPLY • link 5.1 years ago ekl • 0

score 1 · Answer 1 · 2019-11-04

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Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 hours ago

United States

You need to do

library(BiocManager)
install("makecdfenv")
library(makecdfenv)
make.cdf.package("C:\\Users\\EKL\\Downloads\\GPL8345_AFLAVUSa520391F.cdf", "aflavusa520391fcdf", version = "0.0.1", species = "Aspergillus_flavus")
install.packages("aflavus520391fcdf", type = "source", repos = NULL)

And then you should be able to run ReadAffy on the CEL files.

ADD COMMENT • link 5.1 years ago James W. MacDonald 67k

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Thank you so much! I will do so.

ADD REPLY • link 5.1 years ago ekl • 0

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The code below is what I did. I am still having trouble.

library(BiocManager)

install("makecdfenv") Bioconductor version 3.9 (BiocManager 1.30.8), R 3.6.1 (2019-07-05) Installing package(s) 'makecdfenv' trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/makecdfenv_1.60.0.zip' Content type 'application/zip' length 3419205 bytes (3.3 MB) downloaded 3.3 MB

package ‘makecdfenv’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\EKL\AppData\Local\Temp\RtmpE9Qnca\downloadedpackages Old packages: 'BiocManager', 'boot', 'digest', 'foreign', 'hms', 'KernSmooth', 'mgcv', 'nlme', 'rlang' Update all/some/none? [a/s/n]: library(makecdfenv) Update all/some/none? [a/s/n]: make.cdf.package("C:\Users\EKL\Downloads\GPL8345AFLAVUSa520391F.cdf", "aflavusa520391fcdf", version = "0.0.1", species = "Aspergillus_flavus") Update all/some/none? [a/s/n]: install.packages("aflavus520391fcdf", type = "source", repos = NULL) Update all/some/none? [a/s/n]: n

eset<-ReadAffy(celfile.path="C:\Users\EKL\Downloads\GSE57629_RAW") eset AffyBatch object size of arrays=716x716 features (26 kb) cdf=AFLAVUSa520391F (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain AFLAVUSa520391F Library - package aflavusa520391fcdf not installed Bioconductor - aflavusa520391fcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)

ADD REPLY • link 5.1 years ago ekl • 0