microarray data analysis in R
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Entering edit mode
10 months ago

I am following this code for analysis in R of GSE113873 and only getting a symbol mapping to probe only 10 genes and enterzid and not any other why is that

The platform is GPL15207

# install additional bioconductor libraries, if not already installed
BiocManager::install("GEOquery")
BiocManager::install("affy")
BiocManager::install("gcrma")


#Load the necessary libraries
library(GEOquery)
library(affy)
library(gcrma)

if (!requireNamespace("hgu133plus2.db", quietly = TRUE)) {
  install.packages("BiocManager")
  BiocManager::install("hgu133plus2.db")
}
library(hgu133plus2.db)


#Download the CEL file package for this dataset (by GSE - Geo series id)
getGEOSuppFiles("GSE113873")

#Unpack the CEL files
setwd("/Desktop/geodata/")
untar("GSE113873_RAW.tar", exdir = "/Users/charmyshah/Desktop/geodata")

# Load the affy library
library(affy)

# Set the working directory to where the CEL files are
setwd("/Users/charmyshah/Desktop/geodata/GSE113873/")

# List the CEL files in the directory
cel_files <- list.files(pattern = "\\.CEL$")

# Read the CEL files into an AffyBatch object
raw.data <- ReadAffy(filenames = cel_files)


#perform RMA normalization
data.rma.norm=rma(raw.data)

#Get the important stuff out of the data - the expression estimates for each array
rma=exprs(data.rma.norm)

#Format values to 5 decimal places
rma=format(rma, digits=5)


# Look up a few probe IDs in the annotation database
select(hgu133plus2.db, keys = head(probes), columns = c("SYMBOL", "ENTREZID"))

#Extract probe ids, entrez symbols, and entrez ids
probes=row.names(rma)
Symbols = unlist(mget(probes, hgu133plus2SYMBOL, ifnotfound=NA))
Entrez_IDs = unlist(mget(probes, hgu133plus2ENTREZID, ifnotfound=NA))

#Combine gene annotations with raw data
rma=cbind(probes,Symbols,Entrez_IDs,rma)

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microarray • 388 views
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