Hello everyone.
I have an experiment of 5 treatments (including the control) and have checked several genes of interest. Some of these genes were expressed in some treatments but not others. When I graph the results should the treatments with no expression be present and just be blank? What are your suggestions?
Thank you in advance.
Yes, if there is not a single "detect"in the group, then there is no data to show, only the sample size (all of which are then "non-detects").
Hi,
I think whenever there is no change in any gene expression, you may find ct the of that particular gene will almost the same as the control ct. So, upon 2ddct calculation, it will be the value of 1 like control.
Regards
Saurabh
If the gene is not expressed, you don't get a dCt value.
I see 2 options:
1) plot the (individual) dCt values and indicate the number "non-detects" in each group. You can add this number above the data or below the axis labels. Explain their meaning in the figure legend.
2) show only the frequencies of "detects" vs. "non-detects". You can use a frequency (contingency) table instead of a diagram showing dCt values. You can use mosaic plots to visualize such contingency tables.
Saurabh Mandal thank you for your answer, however in some genes there is no expression in my control sample, due to the nature of the research.
Jochen Wilhelm thank you very much. In your first option you mean that I should place the name of the group where there was no detection in the x axis with no ΔCts graphed?
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