delta Cq or delta delta Cq values for scatter plot

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delta Cq or delta delta Cq values for scatter plot

Postby aaronpfrank » Fri Apr 08, 2016 11:07 pm

Hello All,

I would like to see the correlation between two of my genes of interest in a scatter plot; however, I'm confused about which data sets I should use to construct the plots. Is it acceptable to plot the deltaCq values of GOI1 vs the deltaCq values of GOI2 (as would be obtained after the normalization step in GenEx pre-processing)? Or is it better plot the log2 transformed delta delta Cq values (as would be obtained by performing the pre-processing workflow in GenEx)?

Thank you,
Aaron
aaronpfrank
 
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Re: delta Cq or delta delta Cq values for scatter plot

Postby Mikael Kubista » Tue Apr 26, 2016 8:29 am

Both are fine, though they reflect two slightly different things. Plotting Cqs only, may be interesting when comparing two batches or two runs to detect inter run variation. Comparing deltaCq is more relevant when comparing samples.
Mikael Kubista
 
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Re: delta Cq or delta delta Cq values for scatter plot

Postby aaronpfrank » Thu Apr 28, 2016 9:06 pm

Dr. Kubista,

Thank you so much for your guidance. Should the delta Cq's be converted to linear scale using the 2^-deltaCq equation? Furthermore, would plotting delta Cq values versus other parameters (for example, body weight) be appropriate? I think it would be, but would like your opinion.

Thanks,
Aaron
aaronpfrank
 
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