Introduction for Mpeak

Back to Mpeak Ming Zheng's Homepage Email: zmdl@stat.ucla.edu

To use Mpeak software, please follow the following procedure:

1. Double click the program icon to launch the software:

2. Click “file”, then choose “open…” to open the data file. This may take a few minutes for a large data set (~50 MB).

3. Click “Detect Peak” on the menu bar and then choose “triangle shape model” option.

4. A dialog will pop up and you can set the parameters of the model fitting here.

5. Another dialog will pop up and you can set the file to save the result of the fitted shapes (the 2^nd row in the example).

6. One last dialog will pop up and you can set the file to save the result of the identified peaks (the 3^rd row in the example).

Now you are set. Just wait until the program finishes. This may take a few minutes.

Next you can take the output file for numerical analysis directly. If you want to visualize the results, you would need other visualization tools. Currently, we recommend the SignalMap software developed by NimbleGen Inc. For more information about this software, please contact NimbleGen Inc. directly at www.nimblegen.org.

If you need to perform windowing/thresholding step to eliminate un-enriched probes before peak detection, please insert one more step after you load data into memory and before you perform Mpeak algorithm as follows:

1. After loading data into memory as described above, please click the “Probe cluster” item in the menu bar and choose “detect probe cluster”.

2. A dialog will pop up and you can set parameters of windowing/thresholding.

After that, you can click “detect peak” and following the steps described above to perform regular Mpeak algorithm.