Question: Agilent Data Normalization Result
0
gravatar for trandiemnghi
16 months ago by
trandiemnghi0 wrote:

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!

limma arrayexpress agilent • 218 views
ADD COMMENTlink modified 16 months ago by Gordon Smyth37k • written 16 months ago by trandiemnghi0
Answer: Agilent Data Normalization Result
1
gravatar for Gordon Smyth
16 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

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")
ADD COMMENTlink modified 16 months ago • written 16 months ago by Gordon Smyth37k
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