Loading from GEO

This article describes how to prepare a series matrix file from GEO to be loaded to ODM.

Requirements

• Configured odm-sdk. See Configured odm-sdk
• Having pandas library installed. We recommend using the latest version available.
• Data file from GEO, for example GSE29746_series_matrix.txt

Instructions

Run the script providing the GSE29746_series_matrix.txt file as an argument

odm-geo-prepare GSE29746_series_matrix.txt

As a result, the script creates the folder with 3 files (example), that you can use to load to ODM. For example:

├── GSE29746
│   ├── GSE29746_expression.gct
│   ├── GSE29746_samples.tsv
│   └── GSE29746_study.tsv

Load your files to AWS S3 and then to ODM following the instructions