Question: strange intensity decay plot
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gravatar for felix.lappe
7 months ago by
felix.lappe10
felix.lappe10 wrote:

Hi,
I got 6 cel files from an Affymetrix microarray experiment: two conditions and 3 replicates of each condition.

I used the function plotDx from the R package AffyRNADegradation to review the rna degradation and this is what I got: intensity decay plot 101053-01, 101053-02, 101053-03 are replicates of condition 1
101053-04, 101053-05, 101053-06, are replicates of condition 2
x axis shows the 11 different probes and y axis shows the average intensity over all genes.

This looks very different to the plot from the manual: intensity decay plot what it should look like

Now I don't know how to interpret my plot and what I have to do with the data. I'm very confused by the fact that even the order of the different samples is different in each probe. Also the intensity seems to be different depending on the probe.

Does anyone have an idea why the plot looks so strange? Would be very happy if someone could help :)

rna degradation microarray • 231 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by felix.lappe10
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