Run all the code in R_AffyDataProcessingExample.txt.
The output created will help you answer the questions below.
You may need to come up with some code of your own to answer some of the questions.


1]	Comment on each plot that has been produced.
	Tell me as much as you can about each plot:
		why we make it
		what it is useful for in general applications
		what it shows us in this particular example


2]	Are there any outlier arrays in this experiment that you might consider dropping due to experimental artifacts?
	how do we know this?


3]	Is there systematic difference in gene expression between the YNG and OLD groups?
	how do we know this?
	how can we quantifiy this?


4]	How much of the total variance in the data is accounted for by the 2 principle components calculated for this data?


5]	According to the SAM analysis, what is the gene with the single greatest increase in expression in the OLD samples?
		what is it's SAM d-statistic?
		p-value?
		q-value? 
		what is its gene name and gene symbol?


6]	How many genes are selected if an FDR of 0.02 is used as a selection criteria?
	How many genes are selected if an FDR of 0.05 is used as a selection criteria?


7]	Is the Gst gene group differentially expressed?
	How can we determine this?


8]	If we run the geneSetTest() function with its default settings, what statistical test are we applying?


9]	What is the single most extremely regulated gene in the Gst gene group?
	What is its
		d-statisitic?
		p-value?
		q-value?
	Where on the plot of Gst gene SAM d-statisticss does this gene lie?