RMA (Robust Microarray Analysis) is a multi-chip analysis method that when selected, adjusts the probe intensity data in the following three steps:
1) Signal values for each chip are adjusted using RMA background correction.
2) Data across all of the chips is normalized using the selected normalization method:
•Quantile: Adjusts the probe intensity values so that the distribution is the same across all arrays.
•Global Median: Scales the probe intensity values so that the median per array is the same across all arrays. Each experiment in your project will be scaled so that they all have the same median signal value.
•None: No adjustments will be made to the probe intensity values.
3) Probe data are summarized into gene level signal values using RMA’s median polish summarization.
This method is available for probe level data from any manufacturer, providing the probe layout is the same between all of the chips. For example, if one chip has gene A with 20 probes on it, then gene A must also be on all of the other chips in the project and associated with the same 20 probes.
Note: When Global Median is chosen as the normalization method for RMA analysis, a scaling factor is calculated for each chip and displayed in the Experiment Attributes section of the Experiment List View under Preprocessing. This scaling factor can be a useful measure of quality when analyzing and comparing chips.
ArrayStar uses the RMAExpress algorithms (Bolstad, 2004) for its RMA analysis.