[BioC] Affy package

[James MacDonald]

I usually look at this plot as an indication of the consistency of my
samples. The slope(s) will be different depending on the chip you use.
For instance, a really good HG-U95av2 chip will have a slope approaching
zero (for instance, the affy latin square data set are all consistently
near zero). On the other hand, a U133A or U133plus2 will have a rather
steep slope. Therefore, the slope is not necessarily informative.

So rather than use the slope as a quality control metric, I simply look
to see that the chips all have relatively similar slopes, which to me
indicates consistent sample quality. However, I find that this plot is
much less likely to point out a possible problem with my data. The
density plot in my experience is a much better indicator of problematic
chips.

The p-value refers to the test of the null hypothesis that the slope =
0. If you have a very small p-value it indicates evidence that the slope
is not zero.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Mette A. Peters" <mpeters1 at u.washington.edu> 08/16/04 05:36PM >>>
Can someone please explain to me how to interpret the RNA degradation
analysis (plot and slope) in the Affy package. I see little
correlation
between the slope calculated with this tool and the 5'/3' signal
intensity
ratio of the housekeeping genes (such as GAPDH and Actin) on the Affy
arrays.  What slope is considered an indication of degradation?  Can
you
also please explain to me what the p-value refers to.

Thanks,
Mette Peters

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