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I am trying to take data from a microarray dataset and transfer the Probe ID's into their respective gene signals. What am I doing wrong?
Code should be placed in three backticks as shown below
URL <- "https://www.ebi.ac.uk/arrayexpress/files/XXX"
SDRF.file <- "XXX.sdrf.txt"
Data.file <- setwd("/Users/XXX/Documents/XXX (1)")
download.file(paste(URL,SDRF.file,sep="/"), SDRF.file)
SDRF <- read.delim("XXX",check.names=FALSE,stringsAsFactors=FALSE)
SDRF[,c("Array Data File","Factor Value[compound]","Factor Value[dose]")]
Treatment <- SDRF[,"Factor Value[dose]"]
levels <- c("NA","1","4")
Treatment <- factor(Treatment, levels=levels)
x <- read.maimages(SDRF[,"Array Data File"],
source="agilent", green.only=TRUE, other.columns="gIsWellAboveBG")
dim(x)
# include your problematic code here with any corresponding output
library(RnAgilentDesign028282.db)
x$genes$EntrezID <- mapIds(RnAgilentDesign028282.db, x$genes$ProbeName,
keytype ="PROBEID", column ="ENTREZID")
x$genes$Symbol <- mapIds(RnAgilentDesign028282.db, x$genes$ProbeName,
keytype="PROBEID", column="SYMBOL")
x$genes[201:205,]
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'PROBEID'. Please use the keys method to see a listing of valid arguments.
# please also include the results of running the following in an R session
sessionInfo( )
Could you please show the output of the following commands: