Statistical Question
adam at tcgu.med.utoronto.ca
adam at tcgu.med.utoronto.ca
Wed Aug 4 17:38:04 EST 1999
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
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