I need to do protein-protein interaction network analysis for which dataset was downloaded from GEO datasets. Data is in the .cel format. I am unable to read these files. Please also suggest "How to apply gcrma package on data?"
I have GSM358670 in .cel format and I am getting an error like
read.celfile(GSM358670)
Error in read.celfile(GSM358670) :
STRING_ELT() can only be applied to a 'character vector', not a 'list'
Hi
Firstly, you need to install several R packages, including "affyPLM" and "affy".
R code (To install packages):
###############
source("http://bioconductor.org/biocLite.R")
biocLite("affy")
biocLite("affyPLM")
###############
Then, you should put all the .cel files into one folder and set the folder as the work directory in R environment.
Finally, load the two R packages and process the .cel files.
R code (load the packages and process the .cel files):
################
library(affyPLM)
library(affy)
Data
Hi
Firstly, you need to install several R packages, including "affyPLM" and "affy".
R code (To install packages):
###############
source("http://bioconductor.org/biocLite.R")
biocLite("affy")
biocLite("affyPLM")
###############
Then, you should put all the .cel files into one folder and set the folder as the work directory in R environment.
Finally, load the two R packages and process the .cel files.
R code (load the packages and process the .cel files):
################
library(affyPLM)
library(affy)
Data
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