Cvt2Mae Data Conversion Steps Description

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The Cvt2Mae "Wizard"

You should use the Cvt2Mae program to convert your data to the MAExplorer format. Cvt2Mae has a multi-step process (wizard) that allows you to create an Array Layout that describes your data. One could edit the raw data files by hand but this is tedious and prone to errors. NOTE: The step titles below are links to in depth descriptions.

Step 1 Select Array Chip (Array Layout)
Cvt2Mae has several predefined Array Layouts (Affymetrix, GenePix, Scanalyze and others) available from a pull down menu. One can also create, edit and save their own custom Array Layouts using the <user-define> Array Layout.

Step 2 Select input file(s)
Some arrays may have several data files, such as a separate GIPO file or separate spot quantification files. Some files have multiple samples within each file. You can also pick multiple data files to convert. Cvt2Mae has the flexibility to handle complex data files.

Step 3 Edit Array Layout
For <user-defined> arrays, you must first define some parameters such as array geometry, which row contains the fields, if it is Cy3/Cy5 data or intensity data etc. before converting data. Also, if you are using one of the predefined Array Layouts and your data is slightly different you will have to edit the Array Layout to correct these differences. These parameters are described in detail in Appendix A. The Array Layout can then be saved and used many times for other data files with the same data format.

Step 4 Choose output folder/directory
This is the project directory where the converted data files will be saved and used with MAExplorer.

Step 5 Convert Data
The last step is to click the "Run" button which starts the data conversion. Several folders are created in the project directory to hold the converted data. Once this is completed, the "Run" button will turn into a "Done" button which you press to exit the program. You can now go the newly created MAE sub directory and click on the Start.mae file (assuming you have installed MAExplorer) to start MAExplorer on your converted data.

Status Window and Help

There are 3 message areas at the bottom of the Cvt2Mae window that are used for reporting error and status messages. If certain parameters are not consistent, error messages will appear in the message area along with suggestions on how to correct the problem.

The Edit Layout wizard also has its own information area that is used for reporting. When you hold the mouse over the a field on the left side of the wizard window, information about that parameter will appear in the lower message area.

Generation of a pseudoarray geometry if no array geometry is specified

MAExplorer requires the data in the GIPO and Quant files be specified by a spot position. This is indicated by the array spot geometry of (#fields, #grids, #rows/grid, #columns/grid). The #fields is the number ofof duplicated sets of grids if available - it is 1 otherwise. This 4-tuple must be specified in the Configuration file. However, some array data does not have a spot geometry position data available. The alternative is to generate a pseudoarray geometry. This is possible since the pseudoarray image in MAExplorer is used simply to indicate success of the data filter or relative differences depending on the "Plot | Show Microarray" option. The algorithm presented below will generate a geometry (nGrids,nGridRows,nGridCols) that is compatible with the visual use of the pseudoarray. The only assumption is the nRowsExpected, the number of spots in the microarray (rows in the database input file). The number of spots in the array is computed automatically and the option to use the pseudoarray instead of the actual array geometry is selected in the Edit Layout Wizard for Grid Geometry.

    OPT_GRID_SIZE = 1200;                /* Optimal grid size for MAExplorer viewing */
    ROWS_TO_COLS_ASPECT_RATIO = 3.0/4.0; /* desired rows/cols aspect aspect for a grid */ 
    extra = 0;                           /* # of extra grid cols required */ 
    /* Estimate # of grids. Assume a square aspect ratio */ 
    if(n <= OPT_GRID_SIZE)
      nGrids = 1;
      nGrids = (n / OPT_GRID_SIZE)+1;
   /* Estimate rows (r) and columns (c) from a rectangular grid 
    * where cols = (4/3) rows.
    * Then, c = (4/3)r and r*c= area. 
    * Then (4/3)*r*r = area or
    * r = sqrt((3/4)*area).
   if(nRowsExpected > 0)
       { /* iterate to optimal size */
	 gridSize = n/nGrids;
	 nGridRows = sqrt( ROWS_TO_COLS_ASPECT_RATIO * gridSize );
	 nGridCols = (nGridRows / ROWS_TO_COLS_ASPECT_RATIO);
	 nGridCols += extra;
	 estTotSize = (nGrids * nGridRows * nGridCols);
        if(estTotSize > nRowsExpected)
	  extra++;                       /* keep trying until meet criteria */
       } /* iterate to optimal size */

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