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, that you can use to load to ODM. For example:

├── GSE17748
│   ├── GSE17748_expression.gct
│   ├── GSE17748_samples.tsv
│   └── GSE17748_study.tsv

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