Entering edit mode
I am not able to do this can someone explain what should I do to solve this issue
Code should be placed in three backticks as shown below
library(tibble)
library(GEOquery)
library(limma)
library(umap)
library(tidyverse)
library(affy)
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::install("hgu133plus2.db")
BiocManager::install("hgu133plus2cdf")
BiocManager::install("hgu133plus2probe",force=TRUE)
library("hgu133plus2probe")
library("hgu133plus2cdf")
library("hgu133plus2.db")
#gset is assigned the value of variable that is the data that is being accessed
#GSEmatrix=True means soft files are being opened
#Contains DataSet information, experiment variable subsets, expression value measurements and gene symbols
#AnnotGPL means that
#A boolean defaulting to FALSE as to
#whether or not to use the Annotation GPL information.
#These files are nice to use because they contain up-to-date information remapped from
# Entrez Gene on a regular basis. However, they do not exist for all GPLs; in general,
#they are only available for GPLs referenced by a GDS
# load series and platform data from GEO
getGEOSuppFiles("GSE28829")
#untar files, since files are in a compressed format
#the files are being extracted in the external directory called data
untar("GSE28829/GSE28829_RAW.tar",exdir='data/')
#reading in cells files using the affy package and providig teh path and store it in variable which is raw data object
raw.data <-ReadAffy(celfile.path = "data/")
#rma normalisation
normalized.data<- rma(raw.data)
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
> library(GEOquery)
> library(limma)
> library(umap)
> library(tidyverse)
> library(affy)
> if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10)
Old packages: 'boot', 'class', 'cluster', 'digest', 'foreign', 'ggpp', 'htmltools', 'jpeg', 'jsonlite', 'lattice', 'MASS',
'Matrix', 'mgcv', 'nlme', 'nnet', 'openssl', 'png', 'rpart', 'sass', 'spatial', 'stringr', 'survival', 'testthat', 'XML'
Update all/some/none? [a/s/n]:
n
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10)
Old packages: 'boot', 'class', 'cluster', 'digest', 'foreign', 'ggpp', 'htmltools', 'jpeg', 'jsonlite', 'lattice', 'MASS',
'Matrix', 'mgcv', 'nlme', 'nnet', 'openssl', 'png', 'rpart', 'sass', 'spatial', 'stringr', 'survival', 'testthat', 'XML'
Update all/some/none? [a/s/n]:
n
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10)
Old packages: 'boot', 'class', 'cluster', 'digest', 'foreign', 'ggpp', 'htmltools', 'jpeg', 'jsonlite', 'lattice', 'MASS',
'Matrix', 'mgcv', 'nlme', 'nnet', 'openssl', 'png', 'rpart', 'sass', 'spatial', 'stringr', 'survival', 'testthat', 'XML'
Update all/some/none? [a/s/n]: BiocManager::install("hgu133plus2.db")
Update all/some/none? [a/s/n]: BiocManager::install("hgu133plus2cdf")
Update all/some/none? [a/s/n]:
n
> BiocManager::install("hgu133plus2probe",force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10)
Installing package(s) 'hgu133plus2probe'
installing the source package ‘hgu133plus2probe’
trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz'
Content type 'application/octet-stream' length 8505171 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
* installing *source* package ‘hgu133plus2probe’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning messages:
1: package ‘AnnotationDbi’ was built under R version 4.1.2
2: package ‘S4Vectors’ was built under R version 4.1.3
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: package ‘AnnotationDbi’ was built under R version 4.1.2
Warning: package ‘S4Vectors’ was built under R version 4.1.3
** testing if installed package can be loaded from final location
Warning: package ‘AnnotationDbi’ was built under R version 4.1.2
Warning: package ‘S4Vectors’ was built under R version 4.1.3
** testing if installed package keeps a record of temporary installation path
* DONE (hgu133plus2probe)
The downloaded source packages are in
‘/private/var/folders/lm/38qkbylx6rzbmkpdcywfhxcw0000gn/T/RtmpLLvcTY/downloaded_packages’
Old packages: 'boot', 'class', 'cluster', 'digest', 'foreign', 'ggpp', 'htmltools', 'jpeg', 'jsonlite', 'lattice', 'MASS',
'Matrix', 'mgcv', 'nlme', 'nnet', 'openssl', 'png', 'rpart', 'sass', 'spatial', 'stringr', 'survival', 'testthat', 'XML'
Update all/some/none? [a/s/n]: library("hgu133plus2probe")
Update all/some/none? [a/s/n]: library("hgu133plus2cdf")
Update all/some/none? [a/s/n]:
n
> # load series and platform data from GEO
> getGEOSuppFiles("GSE28829")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28829/suppl//GSE28829_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 157736960 bytes (150.4 MB)
==================================================
downloaded 150.4 MB
size isdir mode mtime ctime
/Users/charmyshah/GSE28829/GSE28829_RAW.tar 157736960 FALSE 644 2022-12-12 10:50:20 2022-12-12 10:50:20
atime uid gid uname grname
/Users/charmyshah/GSE28829/GSE28829_RAW.tar 2022-12-12 10:50:17 501 20 charmyshah staff
> untar("GSE28829/GSE28829_RAW.tar",exdir='data/')
> #reading in cells files using the affy package and providig teh path and store it in variable which is raw data object
> raw.data <-ReadAffy(celfile.path = "data/")
> #rma normalisation
> normalized.data<- rma(raw.data)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain 2.0
Library - package 2.0cdf not installed
Bioconductor - 2.0cdf not available
sessionInfo( )
r version 4.1.1
