Tiling Array Analysis



At the top of the control panel is a popup menu for selecting the sequence (chromosome, plasmid 1, plasmid 2, ...) as configured in the new project wizard.

Display Tracks

Next is a menu of tracks to display. Clicking in the checkbox next to each item toggles its display in the Main Display. The tracks are displayed in the Main Display in the same order as they are listed in the display tracks menu.

If you control-click on any of the available tracks, GenomeMTV will display a popup menu for generatting additional plots. The Details choice opens a separate window with a spreadsheet displaying the numeric values for each plot, and allows you to sort and save the values in a variety of formats. (See Spreadsheet below). The Density choice displays a density plot of the distribution of signal intensities. (See Density Plot below)

The available plots are:

Control Panel

Main Display

The project display window is divided into 2 main regions, with the Control Panel on the left, and the Main Display on the right. The Control Panel has options for selecting the molecule, plots, and parameters to display, and can be used for updated the thresholds used by Tadpol for determining polymorphic regions. The Main Display has several synchronized graphical views of the data, displaying synchronized tracks with signal intensity, polymorphism predictions, and gene locations positioned along the reference sequence.

Control Panel

The main display has several synchronized tracks as enabled in the control panel. Each plot is labeled to with the same names and in the same order as in the control panel. At the bottom of the display is a range slider that can be used to zoom or scroll the display. All of the tracks will be simultaneously adjusted and remain vertically aligned.

Pressing control-click allows you to drag a rectangle to zoom into the plot at a specific location. Option-click and dragging scrolls the display to the left or right. Clicking in a plot and then pressing ‘l’ displays a legend of what the different colored tracks represent. Mousing between the different tracks changes the mouse to a grip adjustment tool, and allows for resizing the different tracks.

Under the “File” menu is an option to “Save Image”. This option saves the current view to a PNG file suitable for publication. There is also an “Export Polymorphisms” option, which allows you to save the predicted polymorphic regions for the currently selected molecule to a simple text file suitable for loading in Excel or other spreadsheet programs. The “Options” menu has advanced options for making adjustments to the display. The “Window” menu has options for changing the currently visible window when multiple window are displayed.

Navigation Controls

Select: Mouse, Mouse + Cmd toggles selection

Pan: Mouse + Alt, Middle Mouse

Zoom box: Mouse + Ctrl, Right Mouse

Zoom keys: ‘U’ unzoom, ‘+/–’ zoom in/out, ‘P’ previous zoom, ‘N’ next zoom

Feature tabbing: ‘[‘ jump to last feature, ‘]’ jump to next feature

Toggle Grid: ‘G’

Main Display


  1. -Smoothed Median QNormalized Signal: The smoothed average reference (red) and query (blue) signal intensity at each position in the genome.

  1. -Ref QNormalized Signal: The quantile normalized signal intensities for each reference chip. Each chip is displayed in a different color

  1. -Qry QNormalized Signal: The quantile normalized signal intensities for each query chip. Each chip is displayed in a different color.

  1. -Ref Lg Signal: The log base-2 signal intensity for the reference chips. Each chip is displayed in a different color.

  1. -Qry Lg Signal: The log base-2 signal intensity for the query chips. Each chip is displayed in a different color.


For all tadpol plots, green indicates the signal is within a gene region, and yellow is intergenic.

  1. -Smoothed SNP Likelihood Ratio: Smoothed SNP likelihood ratio for the likelihood there is a SNP at the given position according to the tadpol scoring algorithm.

  1. -Smoothed Log Ratio QNormalized Signal: Smoothed version of the Log Ratio QNormalized Signal which is the log ratio of the median qnormlized signal intensity values for the reference and query chips, i.e., the difference between the smoothed median qnormalized signal values.


  1. -Predicted Polymorphisms: Regions scored by tadpol as polymorphic

  1. -Genes: Gene regions on the sequence as specified in the annotations file

Tadpol Parameters

Next are the Tadpol parameters, which specify the thresholds for determining if the signal differences are significant enough to declare a polymorphic region.

  1. -Score Threshold: The minimum SNP Likelihood ratio necessary for declaring a polymorphic region.

  1. -Peak Sharpness: The minimum sharpness to SNP Likelihood ratio score for a polymorphic region, as measured by the discrete derivative of the peak.

  1. -Min Width: The minimum width of a polymorphic region

  1. -Merge Limit: Polymorphic regions within this threshold distance apart are merged into a single region.

The “Update” button recomputes the polymorphic regions based on the current parameters.

Tadpol Summary

At the bottom of the control panel is a summary of the Tadpol predicted polymorphic regions. The values are:

  1. -Count: The number of polymorphic regions

  2. -Range: The size of the smallest and largest polymorphic region

  3. -Mean Len: The mean and standard deviation size of the polymorphic region

  1. -Median Len: The median polymorphic region size

  1. -Total Len: The total length of all of the polymorphic regions

Range Slider

Control-clicking on a track in the control panel displays a popup menu for additional plots. The Details choice displays a spreadsheet of the selected item, with a textual display of the information. The spreadsheet has menu choices for exporting the data to a text file, and the rows can be sorted by clicking on a header column. For example, to find the largest polymorphic region, display the details for the Polymorphic Regions track, and then sort by the length column.


Control-clicking on a track in the control panel displays a popup menu for additional plots. The Density choice displays a density plot (smoothed histogram) for the signal intensity values, showing the fraction of points with a particular signal strength. This can be used to visualize the skew in a given chip, or the effectiveness of the quantile normalization. The popup menu for the polymorphic regions item has separate density plots for the lengths of the polymorphic regions. the maximum tadpol score of each region, and the maximum sharpness of each region.

Density Plots


- Control Panel

- Main Display

- Spreadsheets

  1. -Density Plots

  2. -Calibration

Tadpol Calibration

It is possible to calibrate Tadpol parameters by importing known polymorphism data. Select “Import Polymorphisms” from the “File” menu to load a table of known polymorphisms for the current molecule. This file must be tab delimited and contain 4 columns: START, END, TYPE, GOOD. START and END are the boundaries of the polymorphism on the reference molecule. TYPE can be either (S) for SNP, (I) for insertion in query, or (D) for deletion in query. GOOD can be either 1 or 0, with 1 reserved for high-confidence polymorphisms and 0 for low-confidence polymorphisms. Imported polymorphism data will be displayed alongside the predicted polymorphisms.

    Using imported polymorphism data, GenomeMTV computes the accuracy of the predicted polymorphisms. High-confidence polymorphisms are compared against the predicted regions to compute the true-positive and false-positive rates. Predicted polymorphisms coinciding with low-confidence polymorphisms are ignored from the computation, i.e. not included in either the false- or true-positive rates. To view a receiver operating characteristic (ROC) curve, press the “ROC” button that appears in the control panel after the polymorphisms have been loaded.