Measurement data and specifications of data processing

The section about measurements describes the data that was obtained as a result of the hybridization process(es) and consists of three parts: the raw data originating from scanning: the intensities measured by the image analysis; and the gene expression levels after normalization and transformation.

1. The minimum information about the raw data is:

• the hardware used for scanning (make and model);

• the software used for scanning;

• a detailed protocol describing the scanning process including scan parameters (laser power, spatial resolution, pixel space, PMT voltage);

• (the image file resulting from the scanning of the hybridized micro-array).

There is no consensus among MGED as to whether the scanned image files are part of MIAME or not.

2. The minimum information about the measured intensities is:

• the complete output of the image analysis software for each element;

• used image analysis software, version and availability;

• parameters used for the image analysis.

3. The minimum information about the data transformation process is:

• the gene expression data matrix summarizing related elements;

• a detailed description of the data selection and transformation procedures;

• some reliability indicators for each data point (e.g. standard deviation).

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