Overview of Steps
If you start with two tiff files, you will need to perform the following steps in order to produce clusters or explore your data.
1) Start a Project
2) Add files to project (recommended)
3) Load tiff files
4) Load gene list
5) Locate spots (Gridding and Addressing)
6) Distinguish signal from background and generate expression file (Segmentation)
7) Repeat steps 1-6 for all experimental conditions, appending to previous data and forming an expression file with several columns
8) Log-transform ratios
9) Add gene info to expression file (optional)
10) Explore data (recommended)
11) Filter data (recommended)
The following steps can only be performed if you have three or more columns in your expression file:
12) Calculate dissimilarity (e.g. 1 - correlation)
13) Cluster genes