Statistical Question

[adam at tcgu.med.utoronto.ca]

Hello, 

I have a couple of stats questions.  First, I am trying to use the Chi
Square test to compare the level of gene transcription for a number of
different genes between two different tissue samples.  One problem I
am having is I don't know what to do in the situation when one sample
has a value of 0 and the other does not.  Specifically, this results
in an expected value of 0.  

Second, I don't even know if I can use this test for my comparison.  I
am using the following formula --- (observed-expected)^2/expected
I assume I use a degree of freedom=1 as I am looking at individual
genes.  Also, I have seen examples where this test has been used with
expected values <5, but I have read that this test is unreliable in
situations when the expect is <5.



I will give a sample of my data:
			"# of transcripts"
		Normal		Diseased
gene1		2		4

frequency	2/6500		4/5000

Expected	(2/6500)*5000= 1.54

Chi Squared   (4-1.54)^2/1.54 = 3.93

gene2		0		12

Now what???


Any suggestions?  Please help me if you can.



adam dempsey
adam at tcgu.med.utoronto.ca