From BITS wiki
Jump to: navigation, search

Source Source

Simple Omnibus Format in Text (SOFT) is designed for rapid batch submission (and download) of data. SOFT is a simple line-based, plain text format, meaning that SOFT files may be readily generated from common spreadsheet and database applications. A single SOFT file can hold both data tables and accompanying descriptive information for multiple, concatenated Platforms, Samples, and/or Series records. Used by GEO.

There are actually four types of GEO SOFT file available:

GEO Platform (GPL) These files describe a particular type of microarray. They are annotation files.

GEO Sample (GSM) Files that contain all the data from the use of a single chip. For each gene there will be multiple scores including the main one, held in the VALUE column.

GEO Series (GSE) Lists of GSM files that together form a single experiment.

GEO Dataset (GDS) These are curated files that hold a summarised combination of a GSE file and its GSM files. They contain normalised expression levels for each gene from each sample (i.e. just the VALUE field from the GSM file).


See example and explanation