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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.
To upload the file, click the "Browse..." button near field "Upload new data file". If you need normalization, check the "normalize" box. If you need split-normalization, use 2nd column of the input file for array index and check the "split-normalize" box. 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 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 "1-color arrays".
For this example there are 2 experiments (2 tissues), with 3 replications in each. Thus the table of experiments should look like this:
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!
If you use subreplications, then fill out the bottom table. Otherwise leave it blank. For example, if each replication had 2 technical subreplications (i.e., each biological sample was hybridized twice), then the input file would have 12 data columns instead of 6. Then the lower table will have numbers: 2 2 2 2 2 2. There are 2 tissues, each replicated 3 times, so there are 6 replications total, and for each we specify the number of subreplications.
rep1 rep1 rep2 rep2 rep3 rep3 |
Then the number of colors in array should be set to "2-color arrays". It will be only 1 experiment named "Embryo" with 3 replications. Placenta is then 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. This type of analysis may yield a greater number of significant genes than if you use "1-color array" option.