| 3 | | 1. Originally data in BASE was stored in raw format, and the average method used was arithmetic mean (the latter differs from the current recommendation for raw data, which is to use geometric mean). |
| 4 | | 2. A flag indicating if stored data was raw, stored as log-2, or log-10 values, was introduced in BASE Ticket [http://base.thep.lu.se/ticket/1120 #1120] (The dynamic part of BASE should keep track whether intensity data is in log space or not). See this ticket for a lengthy discussion on the use and storage of transformed data in BASE. Some additions were:[[BR]][[BR]]a. A `BioAssaySet` has a `getIntensityTransform()` method that returns an `IntensityTransform` `enum` object, whose public `Formula.AverageMethod getAverage()` method returns `Formula.AverageMethod.ARITHMETIC_MEAN` or `Formula.AverageMethod.GEOMETRIC_MEAN`.[[BR]]b. Class `VirtualColumn` was extended with statis methods `VirtualColumn channelIntensity(int channel)` [[BR]][[BR]] |
| 5 | | 3. Enum class `IntensityTransform` public `Formula.AverageMethod getAverage()` method does however return `Formula.AverageMethod.ARITHMETIC_MEAN` for data stored in raw format (according to the flag), and `Formula.AverageMethod.GEOMETRIC_MEAN` for data stored in log-2 or log-10 format. This is the opposite to what is recommended to be used in this ticket, for data fetched in raw form. |
| | 3 | 1. Originally data in BASE was stored in untransformed format, and the average method used was arithmetic mean (the latter differs from the current recommendation for untransformed data, which is to use geometric mean). |
| | 4 | 2. A flag indicating if stored data was untransformed, stored as log-2, or log-10 values, was introduced in BASE Ticket [http://base.thep.lu.se/ticket/1120 #1120] (The dynamic part of BASE should keep track whether intensity data is in log space or not). See this ticket for a lengthy discussion on the use and storage of transformed data in BASE. Some additions were:[[BR]][[BR]]a. A `BioAssaySet` has a `getIntensityTransform()` method that returns an `IntensityTransform` `enum` object, whose public `Formula.AverageMethod getAverage()` method returns `Formula.AverageMethod.ARITHMETIC_MEAN` or `Formula.AverageMethod.GEOMETRIC_MEAN`.[[BR]]b. Class `VirtualColumn` was extended with statis methods `VirtualColumn channelIntensity(int channel)` [[BR]][[BR]] |
| | 5 | 3. Enum class `IntensityTransform` public `Formula.AverageMethod getAverage()` method does however return `Formula.AverageMethod.ARITHMETIC_MEAN` for data stored in untransformed format (according to the flag), and `Formula.AverageMethod.GEOMETRIC_MEAN` for data stored in log-2 or log-10 format. This is the opposite to what is recommended to be used in this ticket, for data fetched in untransformed form. |
