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NIA Array Analysis Tool | |
Or a simpler way:
You can always change tissue names after the file was loaded, so you don't need to edit column headers. However, if column headers are correct then you can use the option (checkbox) to use column headers, and then you will not need to edit them after loading.
Note that red and green channels are swapped for the second subreplication, which is a dye-swap. To upload the file, click the "Browse..." button near field "Upload new data file". Do NOT use normalization or split-normalization because 2-color array require a different kind of color-normalization. Agilent scanner software provides color normalization. Then push "Upload" button. After the file is loaded push "Continue". After the file is downloaded, some default parameters are already filled in. However you may need to modify some of them to specify your experiment.
Description. Write a short description of your experiment, e.g., "Embryo vs. Placenta".
Array type. Select the array type that you used. If the array type is not specified then you will not get references to gene symbols and annotations from graphs and tables. However you can upload you own array annotation if you click on the "Add array" button. See array annotation
. Number of colors in the array. Set it to "2-color arrays".
In this example there is only 1 experiment because both tissues are hybridized in 1 array. It can be called "Embryo" and placenta is used as a reference. Thus, change the field from "don't analyze reference" to "analyze reference", then type in "Placenta" into the Reference name field. In other experiments reference is used for normalization purposes (e.g., Stratogene's Universal Mouse Reference), and then the option "don't analyze reference" should be used. In this example there are 3 biological replications. Thus the table of experiments should look like this:
Dye swaps are interpreted as subreplications. Thus you need to fill the bottom table. There is 1 experiment replicated 3 times, so there are 3 replications total, and for each we specify the number of subreplications (i.e., 2). Thus the table of subreplications should have numbers: 2 2 2.
Other parameters can be left with their default values. However in some
special cases you may need to change some of these parameters. Then use
links from parameter names as a guide for changing.
WARNING: Do NOT change parameters if you don't understand their effect on
program performance. First read the description of the parameter!