A beginner's (i.e. wet-bench trained person) question of microarray gene expression analysis -
I downloaded and extracted the "expression values" (or should I call them "signal intensity" ?) of some microarray experiments from GEO access. As I would only be looking at a handful of genes, NOT the whole genome expression, is there a free software, or a free web-based interface that allows me to plug in the "raw values" and tell me if they are statistically different or similar ? Or what would be the "correct" way of doing analyses on these raw values if no easy interface exists to expedite my analysis?
probe HGNC ctrl1 ctrl2 ctrl3 ctrl4 ss1 ss2 ss3 ss4 232546_at TP73 4.76775 3.36975 4.89104 2.96765 4.15112 3.07037 4.52393 4.71372
From what I've read, it seems that I cannot DIRECTLY compare these two sets of value using the simple average(medium value) and t-test. It seems that I need to normalize these values first. Do I need to ? Which control probes should I look for to normalize the gene values? Any direction/solution will be greatly appreciated. My apology if a similar question has been raised in the past (apparently, I am so new to array analyses that I do not know how to ask/find a question).