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Overview
The data files must be in the Axon .gpr file format.
Sample Order
The sample order of imported datasets is determined by the order of the source sample data files listed in the Import Data dialog.
Template |
Result of Import |
GenePix |
Multiple files are processed into a single dataset. |
GenePix Merge Replicates |
Multiple files are processed into a single dataset. |
GenePix Green/Red |
Multiple files are processed into a single ratio dataset (treatment/control). |
GenePix Red/Green |
Multiple files are processed into a single ratio dataset (treatment/control). |
If you are importing using one of the two-color data templates (the dye colors are listed as treatment/control in the template name), all data values <0 are replaced with missing values (null values). Between-chip replicate measurements are imported as samples with the same names.
When the import process is complete, a dataset that is the ratio of treatment/control is added to the Experiments navigator. A selected sample ratio can be displayed in an intensity-bias plot to determine whether Lowess normalization is appropriate for the dataset.
Import Process for GenePix and GenePix Merge Replicates
The file headers are discarded.
Gene identifier information is retrieved from the Name column of the first file and is stored as a GenBank Identifier.
Gene expression data is retrieved from the Ratio of Medians column of each file in the order they are placed in the Import Data dialog.
The resulting dataset is not be amenable to Lowess Normalization or Intensity-Bias plots. See Two-Color Data for more information.
The GenePix Merge Replicates merges any duplicate gene identifiers and computes reliability measures from the spread. See Merging Within-Chip Replicate Measurements for more information.
Import Process for GenePix Green/Red
The file headers are discarded.
The RatioFormulation field is ignored.
Gene identifier information is retrieved from the Name column of the first file and is stored as a GenBank Identifier.
The control (green dye) expression data is calculated by subtracting the B532 Median column from the F532 Median column.
The treatment (red dye) expression data is calculated by subtracting the B635 Median column from the F635 Median column.
The resulting dataset is amenable to Lowess Normalization and Intensity-Bias plots.
Import Process for GenePix Red/Green
The file headers are discarded.
The RatioFormulation field is ignored.
Gene identifier information is retrieved from the Name column of the first file and is stored as a GenBank Identifier.
The control (red dye) expression data is calculated by subtracting the B635 Median column from the F635 Median column.
The treatment (green dye) expression data is calculated by subtracting the B532 Median column from the F532 Median column.
The resulting dataset is amenable to Lowess Normalization and Intensity-Bias plots.
Related Topics:
Selecting a Template for Data Import
Importing Multiple Files With One Sample Each
Merging Within-Chip Replicate Measurements