Is it normal that my RNA degradation plot shows more degradation at the 3'-end?
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8.6 years ago
Juan Cordero ▴ 140

Dear comm,

I have made a RNA degradation plot with the function plotAffyRNAdeg from affy package (Bioconductor) and it seems RNA is more degraded at the 3'-end compared with the 5'. What does it mean? Should I trust my results? Should I correct anything?

BTW, all p-values from summaryRNAdeg function are below 0.05.

Thanks in advance

Bioconductor Affymetrix Microarray R • 1.8k views
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Show the figures so others can give their opinion.

But in general, RNA quality towards 3'ends are of lower quality with respect to 5'-ends.

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image: drosophila_RNAdeg

I get a plot with an opposite trend to this one: lower values in the x-axis get higher values in the y-axis, and vice versa.

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