CDf files in R
1
0
Entering edit mode
ekl • 0
@ekl-22229
Last seen 4.4 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 • 1.6k views
ADD COMMENT
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
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
1
Entering edit mode
@james-w-macdonald-5106
Last seen 59 minutes 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
0
Entering edit mode

Thank you so much! I will do so.

ADD REPLY
0
Entering edit mode

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

Login before adding your answer.

Traffic: 944 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6