structure of SOFT files
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8.8 years ago
vahideh ▴ 20

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!

.soft R GEO • 3.2k views
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8.8 years ago

See here for importing GEO files into R:

http://bioconductor.org/packages/GEOquery

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Thanks Davis!

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

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What problems did you have?

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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!

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