Need help in extract and save expression data from Agilent

Question

[BioMed]

Dear all,

I have a set of data from "Agilent-012391 Whole Human Genome Oligo Microarray G4112A". I used Agilp package to extract and save gene expression data.

The below is the code I used as provided by the author.

library(agilp)
inputdir<-file.path(system.file(package="agilp"),"extdata","", fsep = .Platform$file.sep)
outputdir<-file.path(system.file(package="agilp"),"output/", "", fsep = .Platform$file.sep)
AAProcess(input = inputdir, output = outputdir, s = 9)

This is the error: "Error in [.data.frame(data, , "ProbeName") : undefined columns selected".

Any comments are greatly appreciated.

[zizigolu]

robina user interface software can analyze agilent data

[lakhujanivijay]

Are you looking at the feature extracted text file? Also, is it public data?

If it's public, please share the file link; if not, can you paste first few lines (including headers) of your file here?

Answer 1

[dxf5729]

first have u confirmed that

1. the input directory must have ONLY the data files to be analysed

2. are ur files in the path where ur agilp package is ?