Expression File

Expression file

Purpose: This file contains the measurements of a study; in RNA-Seq, this would be the expression of your cells. The values are used throughout the study in many visualizations. Although the units of the expression data are up to the author of the study, we recommend some variant of log2(TPM +1). You will be able to indicate what format you are uploading in the upload wizard so that, when viewing expression, the axes are correctly labeled. We encourage you to also upload a raw matrix of measurements (like a count matrix), this can be done as a miscellaneous file in the wizard.

Accepted formats:

Expression Matrix (aka dense matrix)
A tab or comma delimited file with columns as cells, rows as genes. The first column should be gene names, the first row should be cell names. When defining names, please use alphanumeric characters; underscores are also valid. Please note, cell names and gene names should match other cell names or gene names in other study files

Example Expression Matrix File

MM Coordinate Matrix File (aka sparse feature-barcode matrix)
An “MM Coordinate Matrix”, as seen in 10x Genomics, is a Matrix Market file that contains a sparse matrix in coordinate form accompanied by a barcodes file, corresponding to column indices of the sparse matrix and a feature or genes file, corresponding to row indices of the sparse matrix.

# To check the format of your file a dense matrix, use the script verify_portal_file.py
# Requires python 3.x
python verify_portal_file.py --expression-files expression_example.txt