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For my analysis I've performed RT-qPCR and measured fold change of genes as log2. I've been trying to compare gene expression of treated (25 nm PSNP) and control samples across multiple independent genes. Since the genes were independent, I wasn't sure whether it would be accurate to perform an ANOVA, but I performed one anyway so I could still compare treatment and control for each independent gene at the post hoc analysis, and also include bonferroni correction for multiple testing.
So for the post hoc analysis I constructed the following formula:
However, next to the Treated (25 nm PSNP) and Control comparisons, this formula also generates all possible combinations of genes and treatments which I don't want to include in my analysis.
Thus my 2 questions are: 1. Is it right to perform an ANOVA followed by a post hoc analysis to compare treatment and control groups of independent genes (groups)? I figured I could also perform an independent t test for each gene, but I didn't know how to correct for all independent tests afterwards in R. 2. How do I perform a post hoc statistical analysis in R where it only compares Treatment and Control for each indepent gene, instead of going through all possible combinations?
I've included a sneak peak of my datafile so you guys can perhaps get a better grip on my analysis.
Thanks in advance!