angel0071987

I have found that a minor allele confers risk in one population and protection in another - please help to explain why this is different? is it simply due to differences in allele frequencies between the 2 populations, or is there more complex explanation?
Thanks in advance.

i have found for one SNP that the minor allele (A) is the risk allele in population 1, and yet in population 2 the minor allele is the same (A), but in this case it is protective why is this? (the risk and protection was determined by the odds ratio - OR >1 A1 increases risk of disease compared to A2). the SNP found may not be the causative SNP itself but instead be in linkage disequilibrium with an unidentified SNP which may be different in the 2 populations. Could there have been a crossover in one population - if so how would that make the risk SNPs different but minor allele the same?

Hi, so i have performed QPCR on some tissue (induced and control). I had 5 different dogs from which i took tissue. I then grew the cells to confluence, and set up an experiment either induced or normal/control in triplicate on three seperate days.
I had 2 reference genes of which i found the geometric mean, and then i worked out for each sample
CT,
Delta CT (CT gene of interest - CT geomean ref gene)
Delta Delta CT (Delta Ct induced - Delta CT normal)
and fold change (2^-DeltaDelta CT)

i averaged the induced and normal fold change at the very end, to get the averga fold change for each gene under the induced and normal condition from which i used to draw graphs etc.

My problem now is how to i tell if the fold change is significant or not - which significant test should i use?

I would assume that the data is not normally distributed so it would have to be a non-parametric test, and i was assuming that the Man Whitney U test would be appropiate, but when i try and run this in  minitab on the fold change values for a gene, it will not run, as the fold change for the control is 1 for every sample - could i therefore run the test on the CT values or DeltaDelta CT values instead?

If anyone could give me any help on how to assess significance of the data (i have minitab and graphpad prism as stats/graphing programs) then it would be much appreciated.

Thank You