Tabular

If you have a data file type that is not supported here, you can define your own file type for importing data. All defined tabular file types will be available from the File Type selection combo box. Select a file type from the selection combo box, or click the File Define Menu button to define a new file type, modify an existing file type or import a user defined file type.

The File Define Menu holds a list of all User Defined File Types. From here you can define new file types, edit a selected file type from the list or delete a selected file type from the list. It is also possible to Import file types defined by others or Export the defined file types so that it can be sent to other people. When you have finished editing your File Define Menu, click OK to go back to the SpotPix Suite.

Click the  Create New or Edit Selected button to open the Define File Type window.

Fill in the File Type Properties to define the file type.

• Name : the name will be added as an identifier of this file type to the File Type combo box in the Data Tab in SpotPix Suite.
• Column Delimiter : The columns can be delimited by either tabular, comma or space.
• Header Row :
  • Row Containing: Type the headers for this filetype, separated by commas.
  • Row Nr.: If you know the header row to always start on the same row number, you can select this option and enter therow number.
  • Header Keywords: If you drag and drop files into the SpotPix Suite Experiment Design area when setting up the experiment, the header keywords typed in this text field will be used to identify the file type.
  • Line Search limit: Normally the header row is found somewhere near the top of a file. Some files can be quite large, and searching through the entire files for the header keywords can be time consuming. It is therefore a good idea to set a limit for how many lines of a file should be searched. If no hit on the header keywords are found within the first e.g. 50 lines, the file will be reported as unknown file format.
• Start Row : The index number of the first data row
  • Header +: use this if you do not know the exact row number, but you know that the first row starts a certain number of rows after the header row.
  • Row Nr: If you know the first data row to always start on the same row number, you can select this option and enter the row number.
• End Row
  • End of file : end row is the last row in the file.
  • Empty Line: end row is the last row before an empty line.
  • End of file - : end row is a certain number of rows before end of file, ie: end of file minus a certain number of rows.
  • Row Containing : end row is a row containing a specific text or a regular expression.
• Comment : short description of this file type.
• Id Header Name (optional) : the name of the column containing the spot identifications
• Identifiers headers (comma delimited) : type the header of the identifier columns in this text field, and separate each header by a comma.
• Suggested Data Columns: here you can set default columns to use for a particular filetype. When a file is dropped into the SpotPix Suite Experiment Design area when setting up the experiment, the default suggested data columns will automatically be set for channel 1 and channel 2.
• Other Elements (optional)
  • Block Header Name : this column holds which array block a spot belongs to.
  • Row Header Name : this column holds which array rows a spot belongs to.
  • Column Header Name : this column holds which array column a spot belongs to.
  • Spot X Header Name : this column holds the x coordinates of the spots. This will be used by the Quality Control component to identify where the spots are.
  • Spot Y Header Name : this column holds the y coordinates of the spots. This will be used by the Quality Control component to identify where the spots are.
  • Flags : this contains information on whether the spots are flagged or not.

You should now test your file format. Click the    Open (Choose a test file) button. See that the Test File Not Set label changes to Test File Set, and click the    Parse button. The result will be displayed in the lower part of the window. If everything looks as you expected, click OK. If it doesn't look as it should, check that all your parameters are entered correctly. Remember that all Header Names must be entered exactly as they appear in the file.

Experiment/Array (Data Tab SpotPix Suite)

Except for a couple of things, the rest of the experiment setup for user defined data type is very much like GenePix data type.

If your dataset have only one channel, check the Single Channel check box, and set which array you want to use as a base sample for log ratios and normalizations. Set the preferred selection for Channel 1.

If your dataset have two channels, see that the Single Channel check box is unchecked. Set the preferred selection for Channel 1 and Channel 2.

Note: No objects can be saved to the Project Dataset data source type.

Quality Control

The Quality Control of User Defined data type is the same as for GenePix.

See SpotPix for filtering and normalization of the data.