In my present study, I am studying the expression of three genes (a,b,c) in NSCLC cases. My goal is to find out if I can classify NSCLC into adenocarcinoma and squamous cell carcinoma based on the Ct value.
1. First I have normalized the Ct value by subtracting the Ct value of endogenous control.
2. I have used a formula to get a score (s) for each case for each gene.
Problem:
1. Should I compare original Ct value or normalized Ct value to understand if there were any significant difference between adenocarcinoma or sqouamous carcinoma for each gene? Which test should I perform (t test or mann-whitney test)?
2. Also, I want to investigate that, if there were any significant difference in Score (S) between adeno and squamous carcinoma for each gene. (Score is derieved from normalised Ct). (Again, should I use t test or mann-whitney test)?
You must do first a normality test(Shapiro) with a qqplot to assess if the distribution is normal. If data is normally distributed, you will use T test. Either way, you will use Mann- Whitney U test
agree with above - how are you using the Ct score to differentiate squam vs adeno?
Try this link
http://stats.stackexchange.com/questions/121852/how-to-choose-between-t-test-or-non-parametric-test-e-g-wilcoxon-in-small-sampl
Sangeet
Please go through the links
http://www.graphpad.com/guides/prism/6/statistics/index.htm?how_the_mann-whitney_test_works.htm
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1120984/
Hope something workout. Good Luck
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