A Measurement represents the collection of results from analysing the scanned image of a microarray after hybridisation. A Measurement can be linked to any number of Property objects, each of which corresponds to one column of data gathered from the image analysis software, or data derived in subsequent analysis such as normalisation.
Examples of data which would be loaded as a 'Property' include signal intensities, signal ratios, pixel counts, quality control statistics.
Property data is loaded from text files (or Excel® spreadhseets) in a similar fashion to loading data in Load mode. Specifying which lines of the file are to be interpreted as data is described here.
Property data consists of two parts, a 'feature name' and a 'property value' - the feature name identifies which feature (i.e. spot) on the array that the property value refers to.
Any number of Property's can be loaded from the same file in one go and extra Property instances can be added to an existing Measurement at any time. This is done by selecting the target Measurement using Edit Mode and pressing the "Add more properties" button.
The "Feature" value is a column specification identifying one or more columns that contain the Feature Name. The Feature names in the file must exactly match the names of the Features that have been linked to the ArrayType used in the hybridisation. Properties do not have to provide values for every feature, but all the feature names that are found in the file must be recognised, otherwise the property will not be loaded.
The "Add a property definition" button adds a set of property description fields to the user interface. Each property has a "Remove this definition" button which removes just that definition, and there is a "Remove all property defintions" button to completely reset the defintions.
The Preset feature allows you to store frequently used settings for later use. The current parsing settings and column specifications can be saved by pressing the "Save current settings as a new preset" button and providing a descriptive name for the saved settings. This name will then appear in the drop-down list. When the name is selected from this list, the previously saved settings will be retrieved.
The remainder of this document describes the collection of values that must be provided for each Property.
Each property is described using the following collection of values
|Column(s)||This value should be a column specification identifying one or more columns that contain the data values for this property.|
|Name||This value specifies a unique identifier for this property. It is required, and each property linked to a Measurement must have a unique name.|
|Unit||This optional value allows the unit (for example 'lumens' or 'pixels') that the property is measured in to be recorded.|
|Scale||This value (which is mandatory) indicates how to interpret the values in the property. The permitted values are "LINEAR, LN, LOG2, LOG10, FOLD_CHANGE, OTHER".|
|This optional link allows the property to be associated with a previously created Labelled Extract.|
|This value describes the class of data that is held in this property, such as measured and derived signal, error, and p-value. (The meanings of the possible values are described below.)|
|This value indicates whether the quantitation has been measured from the background or from the feature itself. The value, which must be provided, can be either "Feature" or "Background".|
The 'Quantitation Type', describing the overall class of the data in property, must be selected from one of the following possible values:
|MeasuredSignal||the best measure from feature extraction as to the presence and intensity of the signal.|
|Ratio||The ratio of two or more signals, typically between two channels.|
|PresentAbsent||Indicates relative presence or absence. Permitted values are "Present, Absent, Marginal, No call, Increase, Marginal Increase, Decrease, Marginal Decrease, No change, Unknown"|
|Failed||Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.|
|DerivedSignal||A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.|
|PValue||Measurement of the accuracy of a quantitation.|
|Error||Error measurement of a quantitation.|
|ExpectedValue||Indication of what value is expected of the associated standard quantitation type.|
|SpecializedQuantitationType||User defined quantitation type.|