# Calculating Relative Expression - how should I analyze my data????? (Jun/12/2008 )

Hello,

I have done qRT-PCR where I have looked at the expression of two separate genes in leukemia samples whose expressions are not the same in the control. I used huPO as my internal control. How do I adjust for this in my analysis? I thought I could just calculate the relative expression and then do a correlation and linear regression and be done. Am I correct or should I do something else?

-flygirl-

QUOTE (flygirl @ Jun 12 2008, 02:23 PM)
Hello,

I have done qRT-PCR where I have looked at the expression of two separate genes in leukemia samples whose expressions are not the same in the control. I used huPO as my internal control. How do I adjust for this in my analysis? I thought I could just calculate the relative expression and then do a correlation and linear regression and be done. Am I correct or should I do something else?

First thing you have to do is calculation of expression index (which is equal to delta Ct, the difference of Ct between the target gene and internal control HuPO)for gene A or B in your samples. Then you can calculate correlation using expression index for gene A and B using spearman correlation analysis.

-larryking-

QUOTE (larryking @ Jun 12 2008, 01:44 PM)
QUOTE (flygirl @ Jun 12 2008, 02:23 PM)
Hello,

I have done qRT-PCR where I have looked at the expression of two separate genes in leukemia samples whose expressions are not the same in the control. I used huPO as my internal control. How do I adjust for this in my analysis? I thought I could just calculate the relative expression and then do a correlation and linear regression and be done. Am I correct or should I do something else?

First thing you have to do is calculation of expression index (which is equal to delta Ct, the difference of Ct between the target gene and internal control HuPO)for gene A or B in your samples. Then you can calculate correlation using expression index for gene A and B using spearman correlation analysis.

Thank you so much for your great advice. I was wondering though, is it possible to also do a pearson's and see which is best?

Thanks,

Amy

-flygirl-

QUOTE (flygirl @ Jun 13 2008, 10:57 AM)
[
Thank you so much for your great advice. I was wondering though, is it possible to also do a pearson's and see which is best?

Thanks,

Amy

If your data belong to normal distribution, it is okay. But based on my experience, spearman is bettter.

-larryking-