structure of SOFT files

Question

[vahideh]

Hi!

I have a GEO file with .soft format, how do I know that this file is one or two channel? can I read SOFT files with read.maimages or ReadAffy functions? The SOFT file structure is confusing me!

Thank you!

Answer 1

[Sean Davis]

See here for importing GEO files into R:

http://bioconductor.org/packages/GEOquery

[vahideh]

Thanks Davis!

I already work with GEOquery, but however, I don't handle it!

[Sean Davis]

What problems did you have?

[vahideh]

I downloaded several GSE files with SOFT format by GEOquery package, then I must implement QC on them. since, As I understood, Quality Control performed differentially between Affymetrix, Agilent and Illumina arrays, so I need to know that I work with which array, and how I Implemented QC on it!