I try to normalize an Agilent dataset from ArrayExpress according to the userguide of limma.

The dataset: http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33005

The code is as follow (exactly the same as in the userguide):

SDRF <- read.delim("E-GEOD-33005.sdrf.txt",check.names=FALSE,stringsAsFactors=FALSE)
x <- read.maimages(SDRF[,"Array Data File"],source="agilent",green.only=TRUE)
y <- backgroundCorrect(x,method="normexp")
y <- normalizeBetweenArrays(y,method="quantile")

But I have a problem like that:

> SDRF <- read.delim("E-GEOD-33005.sdrf.txt",check.names=FALSE,stringsAsFactors=FALSE)
> library(limma)
> x <- read.maimages(SDRF[,"Array Data File"],source="agilent",green.only=TRUE)
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'GSM819076_US10283824_252828210181_S01_GE1_107_Sep09_1_4.txt': No such file or directory

How can I fix it? Thank you!

You are supposed to download the raw data files to your current working directly. You obviously can't read the data files if you don't download them.

The file E-GEOD-33005.raw.1.zip is a zipped archive of all the raw data file. You download that and then unzip it. In R, could you use:

download.file("https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-33005/E-GEOD-33005.raw.1.zip", "raw.zip")
unzip("raw.zip")