The Cvt2Mae "Wizard"

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

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

    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;
    else
      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)
     while(true)
       { /* 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)
	  break;
	else
	  extra++;                       /* keep trying until meet criteria */
       } /* iterate to optimal size */