How do I save my solution ?
    To save your data simply choose the save solution option in the file menu or click on the corresponding icon in the Toolbar. If the option is disabled, you probably have to stop the algorithm first, by using the stop button (see ArrayMiner's Algorithm, Practical Issues). There are four possibilities for saving your data:


  • Clustering save formats
    • Save as ArrayMiner Project (amg extension). This option will save the solution and the algorithm status to the disk.
    • Save as HTML. This option will save the current classification as linked html files. Use the "Preview" button to preview the result in your browser. Or the "Save HTML" button to specify a target folder for the html files. The main page will be named "index.html". You are then free to modify the generated files within your favorite html software. (Note that the profiles will be sorted in the same way as specified in the heatmap view table) More on this topic here
    • Save as GeneSpring Classification File (gsc extension). This will save the solution as a GeneSpring classification file. To open it from GeneSpring, launch GeneSpring, choose the appropriate organism, go to the external program interface and choose the "Load Classification From File" option.
    • Save as ArrayMiner coloring scheme file (amc extension). This will save the current solution in a file you can open with the coloring scheme panel or the classification compare window
    • Save as input CSV. This will generate an input file for ArrayMiner. This format does not include any classification. If you uncheck the "Include Unclassified" checkbox, only the genes assigned to a cluster will be saved. (This checkbox is relevant only in the gaussian mode of the clustering)
    • Save as text file. This will save the result in a tabular text file or copy them into clipboard depending on the chosen button. The data is formatted one gene per line. You can choose to use tab or commas as cell delimiters. Checking the Save Clusters Columns checkbox will add a column with the ID or the name of the assigned cluster. If you check the "Save used data" checkbox, experiments values seen by the algorithm will be added to the file (After normalizations). If you check the "Save raw data" checkbox, experiments values as readed will be added to the file (Before normalizations)

NOTE

    When performing clustering analysis, only the first possibility (ArrayMiner Project) yields a file that contains the full state of the software. (In particular all settings and parameters specified by the user)

NOTE

    When you call ArrayMiner from GeneSpring, and unless you are running Win95/98/Me, your clustering result is also automatically returned upon exit to GeneSpring, where it can then be saved as a regular GeneSpring classification.

 
  • ClassMarker save format

    • Save as an ArrayMiner Project (amp extension) file. This file contains the full project structure and can be reopened in ArrayMiner.
    • Save as Input CSV. This will generate an input file for ArrayMiner. This format does not include any results.If you choose the include only enabled classes option, ArrayMiner will discard all experiments belonging to a disable class.(You can enable/disable a class by using the appropriate checkbox in the Master Tab). You can choose to save the data with the normalized values (as shown in the graphical window) or as raw data using the "Save normalized data" checkbox. If you choose to save the raw data you can include/exclude the genes that did not pass the filter by using the "Include rejected genes" checkbox.
    • Save as an AMC classification. This will generate a clustering coloring scheme file (amc extension) from the current result tab. You can open this file with the coloring scheme panel or the classification compare window. Note that if the same marker appears in different classes, the marker gene will appear in only one cluster of the coloring scheme. You can choose to add the additional markers to the file by enabling the "Include additional markers" checkbox. This save option will be enabled if the master tab is selected.

To learn more about the file extensions, click here.