Loading a Data Set
- In the Multiple Array Viewer, go to File -> Load Data. (There is also a Single Array Viewer that can only open one set of data at a time, but only the Multiple allows you to view many samples together. The real power of MeV is in the program’s analysis modules, found only in the Multiple Array Viewer. That is where the clustering and visualization of data can take place. Therefore, the remainder of this guide will focus on the Multiple Array Viewer. Also, In the Multiple Experiment Viewer, you can go to File ? New Multiple Array Viewer and have more than one experiment window open at a time.)
- When the Expression File Loader comes up, click Browse at the upper right side of the screen.
Tab-delimited file loader
- To choose one of the data sets that were downloaded with the program, choose Desktop from the drop down menu at the top. Open the MeV_4_2 folder, then open the “data” folder. If you have your own data set, find that file on your computer instead.
- Choose a TDMS (Tab Delimited, Multiple Sample) file that ends with *.txt and click Open. (The full MeV manual has a complete list and description of different file formats. The link to the manual can be found at http://tm4.org/mev.html under the heading Appendix: File Format Descriptions.)
- When do I use Annotation? Annotation gives you much more specific information about the gene, which could be more useful down the line.
- To use the automatic Annotation loader, you must be using an Affymetrix dataset. If so, make sure to click the Affymetrix Array radio button. (The program automatically chooses the bubble to the left of Affymetrix Array, the Spotted DNA/cDNA Array or Other Array type, and both cannot be clicked at the same time.)
TDMS loader with data ready to load
- Note that in the sample data, the Affymetrix files have their own folder within the data folder. These have already been normalized. Again, for descriptions on other types of files please see the MeV Manual.
- If you want to use the automatic annotation downloader, you must be connected to the Internet. Click the Connect button. A new screen will pop up with two drop down menus. From the top one, choose the species you are working with, which in the example case is human. Then in the bottom drop down menu choose the correct annotation file, which is the type of chip used in the experiment. This file will begin with “affy” and is found a little further down in the menu. Then click Connect.
- Once the Annotation files are downloaded, click OK to return to the previous screen.
- If you want to use an annotation file from the data folder or from your computer instead, click Browse within the Annotation box and choose the file you want. Then click Open.
- Click the upper-leftmost expression value. That is, under the Expression Table, click the first box that contains a quantitative value. These include columns that contain numerical values such as sample data, but not columns that are labels, names, or other such unquantifiable values. (Note: There may be columns that have 0 or 1 in them to identify data, but are not expression values.)
- Click Load at the bottom of the screen.
- A diagram should come up that looks like lots of tiny green and red boxes. This is the Heatmap View. Each row represents a specific gene, whereas each column represents each sample, or experiment. The lightest green boxes are the most underexpressed genes, the brightest red being the most overexpressed genes. MeV expects that each sample loaded will have the same number of elements, in the same order, and that each gene (or spot) is aligned with that element in every other sample loaded. For example, using that rule, all input files will have data for gene x in row y. Clicking on a rectangle displays a dialog with detailed information about that spot.
- The MeV toolbar on the left hand side should have 5 options. This is called the Navigation Tree. Any heading that has a node to the left of it means that if you double click it, the information within that heading will appear below it. Click Main View to return to the original Heatmap View at any time.
- To find the basic information for the data set, double click Analysis Results ? Data Source Selection Information. This will tell you how many genes are in the data set and how many trials of the experiment were performed with each gene.
- Under History, the History Log will show you which tests were done on the data set and when.