RNA tends to degrade very easily; in general, it degrades from both ends, but worse from the 3' end.
Fortunately, the soybean chips have multiple probes to each gene. There are a variety of reasons for this, but one advantage is that we can ask questions about how degraded the RNA is by comparing the average intensity of spots relative to their position. The RNA degradation plot achieves this.
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Evaluate this code: ## Construct RNA degradation plots and summary library('affy') par(mfrow = c(1,1)) RNAdeg <- AffyRNAdeg(soy.ab) plotAffyRNAdeg(RNAdeg, col = c(rep('blue',3), rep('red', 3))) summaryAffyRNAdeg(RNAdeg)(Complete File)(Rout) The end product should look like this |
There is a lot of debate about how useful these plots actually are. The problem is that, while it's clear that a straight-line would be nice, in practice it never happens, and there are few clear guidelines for how steep a slope is "too bad".
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