Getting Started


The first time you launch GenomeMTV, you’ll see an empty Project Manager. You’ll need create a GenomeMTV Project and load your data.  Click “New” to create the project.

GenomeMTV will ask what type of project you want to create, either a Tiling Array or Gene Expression analysis. After selecting your project type, click “Continue”.

You’ll then be asked to load your chip data. The design file (either CDF or BPMAP file) contains metadata information describing each probe on the array. Click “Select” to display a file chooser and navigate to the design file for the project. The CEL files contain the expression information for each probe on the microarray. Click “Add...” to display a file chooser to load the CEL files. In a Tilling Array project, make sure to mark which CEL files are for the reference chips. After the design file and the CEL files are listed, click “Continue” to load the probe intensity information. It may take several minutes to load the chips if you have a large number of chips in one project.

After the chips are loaded, a dialog will appear asking if you would like to view the QC images for the chips. These images display the probe intensities according to their position on the array, and can reveal spatial or laboratory artifacts on the chips. You should display these images whenever you load a new batch of chips.

Below is a sample QC image. The dark areas in the middle of the chip are expected, and are part  of the design of the chip. The popup menu at the bottom of the dialog switches between different chips.

After closing the QC Raw Chip Image, you’ll return to the Chip Data wizard page. If there were any flawed chips, you can remove those chips by selecting them in the table, and clicking the  “Remove” button. Once you are satisfied with the selection, click “Continue”.

The QC Image dialog will appear again. This time, you should select “No” unless you added additional chips to the project.

Next, the Sequence Data Wizard page is displayed, which allows you to select the probes and molecules of interest. Click the “Add...” button to select the first molecule.

You’ll be asked to select the probe sets for a single sequence. First assign a sequence name, such as “chromosome”. If you have annotation associated with the sequence, click “Select...” to display a file browser, and navigate to the annotation file for this sequence. The annotation file must be tab delimited and contain 4 columns: START, END, NAME, DESCRIPTION.

    Finally, choose the probe sets associated with this sequence. Affymetrix designs usually split the probes for a single sequence into 2 groups for the sense (st) and antisense (at) probes. Make sure to select both sets. Once all of the probes for this sequence are selected, click “Ok”.

After you specify the probe sets for one molecule, you can add additional molecules or remove erroneous probes by selecting the row and clicking “Add...” or “Remove”. After all the molecules are done, click “Continue”.

The final step is to assign your project a name, and specify a location for the project data. Inside the project directory, GenomeMTV will create a file called “TilingProject.mtv” where “TilingProject” is the name you assign, and save all of the project related data there. After you specify the project name and directory, click “Done”.

GenomeMTV will then analyze your CEL files for each sequence and save the results. GenomeMTV will display progress dialogs to inform you of the current molecule and analysis step. It can take several minutes to process your data, depending on how many CEL files your project contains. This analysis is only done once, when you first load the project data, and reused for subsequent visualizations. After the analysis is complete you’ll return to the Project Dialog, and you will see your new Project listed. Click “Open” to display the project.

GenomeMTV will then display the main view. See the Tiling or Expression page for more information.

Click here to download GenomeMTV. The first time you launch PhyloTrac, you'll be asked to register your version. Click here to obtain a registration code.