Statistical analysis of quantitative real-time PCR (qRTPCR) - Statistics on qRTPCR data (Jan/08/2007 )
I have run statistical analysis on fold-changes in a particular gene expression ( n=3 in duplicates). I have two factors in my analysis ( such as STRAIN OF ANIMAL and DAYS OF EXPOSURE TO TREATMENT). Hence I performed two-way repeated ANOVA. Although the fold-changes in gene expression are highly elevated in a particular group ( ex: 100 fold in one group compared to 2-3 in another), I do no thave any statistical significance. I am really puzzled as to how best to represent this biologically relevant yet statistically insignificant data.
why did you choose a repeated ANOVA? Did you take samples from the same animal at different time points? If not, use a 2-way ANOVA for independent samples.
Generally, a two-way ANOVA does three comparisons (Factor 1, Factor 2 and Factor 1 X Factor 2 interaction) which leads to a lot of degrees of freedom and therefore you need a large sample size. Like you experience, even large differences can have very small statistical effect. What to do now? (a) enlarge the sample size, or ( ask the right question (which factor is important?) and test only for this... but a is defenitely preferable! And another short remark - if you use a measure like time as factor, than you'll have a lot of comparisons! Try to build a general linear model with animal strain as fixed factor and time as covariate, this will suit your data better...
Hope that helps,
Thank you very much for your valuable suggestions