Question: run affy package encounts clariomdhumancdf error
0
gravatar for 83310199
6 months ago by
833101990
833101990 wrote:

Hello everyone! I'm going to analyses the CEL files for genes expression information. Run the commands as the affy package's guide pdf provided, some error occurred below:

library(affy) setwd('D://R/affy/') Data <- ReadAffy() eset <- rma(Data)


>library(affy)
>setwd('D://R/affy/')
>Data <- ReadAffy()
>eset <- rma(Data)

Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain ClariomDHuman Library - package clariomdhumancdf not installed Bioconductor - clariomdhumancdf not available


I tried to install the 'ClariomDHuman' package:

library(BiocInstaller) BiocManager::install("ClariomDHuman")


library(BiocInstaller) Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help Warning message: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN package instead. BiocManager::install("ClariomDHuman") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) 'ClariomDHuman' Update old packages: 'openssl', 'purrr', 'rtracklayer', 'tidyr' Update all/some/none? [a/s/n]: a There are binary versions available but the source versions are later: binary source needscompilation openssl 1.2.1 1.2.2 TRUE purrr 0.3.0 0.3.1 TRUE tidyr 0.8.2 0.8.3 TRUE Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/openssl1.2.1.zip' Content type 'application/zip' length 3944621 bytes (3.8 MB) downloaded 3.8 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/purrr0.3.0.zip' Content type 'application/zip' length 413573 bytes (403 KB) downloaded 403 KB trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/rtracklayer1.42.2.zip' Content type 'application/zip' length 3047491 bytes (2.9 MB) downloaded 2.9 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/tidyr0.8.2.zip' Content type 'application/zip' length 948891 bytes (926 KB) downloaded 926 KB package ‘openssl’ successfully unpacked and MD5 sums checked package ‘purrr’ successfully unpacked and MD5 sums checked package ‘rtracklayer’ successfully unpacked and MD5 sums checked package ‘tidyr’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\XiongMing\AppData\Local\Temp\RtmpEXruRI\downloadedpackages Warning message: package ‘ClariomDHuman’ is not available (for R version 3.5.1)

continue to run: eset <- rma(Data)


eset <- rma(Data) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain ClariomDHuman Library - package clariomdhumancdf not installed Bioconductor - clariomdhumancdf not available

What can i do to fix this bug? I'm new to R that I haven't mastered many concepts yet. It would be great if you could give detailed steps and specific guidance. Thank you for your guidance and advice, which will help me get started in the R field.

ADD COMMENTlink modified 6 months ago by Guido Hooiveld2.5k • written 6 months ago by 833101990
Answer: run affy package encounts clariomdhumancdf error
3
gravatar for Guido Hooiveld
6 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

As said in the related thread started by you, and that now is deleted (also by you?!), these are 3rd generation Affymetrix arrays for which NO Chip Definition File (CDF) is available. As a result, these arrays can NOT be analyzed using the library affy, but rather should be analyzed using oligo and the corresponding PdInfo package. Some code to get you started + some relevant links were already provided in the deleted thread....

ADD COMMENTlink modified 6 months ago • written 6 months ago by Guido Hooiveld2.5k

Thank you for your reply, I know that deleting the previous post is not proper, but because I mistakenly described the affy problem as a limma package problem, this makes me look a bit stupid, so I deleted the original post, which may offend you. I am very sorry~

ADD REPLYlink written 6 months ago by 833101990
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