abagen.io.read_microarray

abagen.io.read_microarray(fname, copy=False, parquet=True)[source]

Loads MicroarrayExpression.csv file found at fname

Microarray files contain raw expression data for all the tissue samples taken from a single donor across all genetic probes.

Parameters:

  • fname (str) – Path to MicroarrayExpression.csv file

  • copy (bool, optional) – Whether to return a copy if fname is a pre-loaded pandas.Dataframe. Default: False

  • parquet (bool, optional) – Whether to load data from parquet file instead of CSV. If a parquet file does not already exist then one will be created for faster loading in the future. Only available if fastparquet and python-snappy module are installed. Default: True

Returns:

microarray – Dataframe containing microarray expression data, where P is probes and S is samples. The row index is the unique probe ID assigned during processing, which can be used to match data to the information obtained with read_probes(). The column index is the unique sample ID (integer, beginning at 0) which can be used to match data to the information obtained with read_annotation().

Return type:

(P, S) pandas.DataFrame