Microarray Data - Matching Probe ID's to Gene Expression Symbols
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Entering edit mode
Joshua • 0
@bfff50a9
Last seen 20 months ago
Switzerland

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( )
limma • 706 views
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Entering edit mode

Could you please show the output of the following commands:

head(x$genes)
str(x)
head(keys(RnAgilentDesign028282.db))
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