MultiExperiment Viewer Quickstart Guide MeV软件教程

MeV软件教程

Table of Contents:

I. Preface - 2

II. Installing MeV - 2

III. Opening a Data Set - 2

IV. Filtering - 6

V. Clustering

a. HCL - 8

b. K-means - 11

VI. Modules - T-test – 13

VII. Additional Resources MultiExperiment Viewer Quickstart Guide

MeV软件教程

Preface: This guide is meant to be a quick reference for those who are just beginning to install and use MeV. Any questions that are not answered in this guide are most likely covered in the complete manual.

I. Installing MeV

1. First make sure that Java is properly installed on your computer (not to be confused with Javascript, which is not the same). Java v1.6 or higher for a

Windows PC/Linux and v1.5 or higher for Mac OSX needs to be installed in

order for MeV to work. Go to to get the latest version. Certain MeV modules also require Java 3D, which can be found at .

2. Go to . To begin download, go to the right hand side of the screen and click the “v4.8”link. The browser will be directed to a SourceForge download page specific to the current operating system.

3. A screen should pop up that asks what you want to do with the files. Whether using a PC, Mac, or Linux, open the files and download them.

4. Once downloaded, open the folder and unzip the file.

5. The unzipped folder can be copied to any convenient location on the hard drive.

6. Open the MeV_4_8 folder.

a. Windows users: double click the file called TMEV or tmev.bat to run the program.

b. Linux or Unix users: navigate to the MeV_4_8 folder in a terminal, and

make tmev.sh executable by typing “chmod u+x tmev.sh” then

“./tmev.sh”. MeV can hereafter be run by double-clicking the tmev.sh

file.

c. Macintosh users: double-click the MeV application file.

Loading a Data Set

1. In the Multiple Array Viewer, go to File Load Data. Also, In the Multiple

Experiment Viewer on the main menu bar, go to File New Multiple Array

Viewer and have more than one experiment window open at a time if needed.

2. When the Expression File Loader comes up, click Browse at the upper right side of the screen.

MeV软件教程

3. 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_8 folder, then open the “data” folder. If you have your own data set, find that file on your

computer instead.

4. Choose a TDMS (Tab Delimited, Multiple Sample) file that ends with *.txt and click Open. The one provided with the program is TDMS_format_sample.txt (The full MeV manual has a complete list and description of different file formats. The link to the manual can be found at under the heading

Appendix: File Format Descriptions.)

Making Annotations

Annotation gives you much more specific information about the gene, which could be more useful down the line.

a. To use the Automatic Annotation loader, an Affymetrix dataset must be used.

MeV软件教程

b. 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.

c. To use the automatic annotation downloader, an internet connection is needed. Next, click the Automatically download radio button and check the Load

Annotation check box. In the same panel there will be 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.

MeV软件教程

d. To use an annotation file from the data folder or from your computer instead, click the Load from local file radio button within the Load Annotation Data

box and click Choose File. Then click Open.

5. Once that is completed, whether an annotation was used or not, 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.)

MeV软件教程

6. Click Load at the bottom of the screen.

7. 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.

8. The MeV toolbar on the left hand side should have 5 options. This is called the Result Tree. Any heading that has a node to the left of it means that when double clicked the information within that heading will appear below it. Click Main View to return to the original Heatmap View at any time.

9. 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 p …… 此处隐藏：10648字，全部文档内容请下载后查看。喜欢就下载吧 ……