[BioC] RNA degradation plots

[James MacDonald]

I don't think there is a consensus on what is and isn't 'bad' when
considering the slope of the degradation plots. There was a recent
thread on this list where somebody noted that the U133A chips always
have a positive slope, so you are probably OK.

In my opinion, the slope is not nearly as critical as consistency of
the slopes, especially if you are doing something like rma where you are
considering all the chips as a batch. Since the expression values are
only meaningful when compared to other expression values in that batch,
consistent problems with degradation/second strand synthesis should all
come out in the wash.

One other recourse is to eliminate the first few probes on the 5' end
and see if you get different/better results. This would probably require
some code hacking (I don't think this functionality exists right now),
and you would also have to decide how many probes to remove as well as
come up with some way to detect improvements in the expression values.

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

>>> "Harry Hurd" <hhurd1 at nc.rr.com> 01/08/04 05:45PM >>>
Hello,

We are looking at some HG-U133A arrays in which the RNA degredation
plot shows a large increase from 5' to 3'. Is it neccessarily bad? Is
there a condition on the slope that defines "bad"?

Here are the slopes and pvs.

slope 1.88 1.34 1.86 1.71
pvalue 1.94e-07 3.74e-05 1.14e-07 6.48e-07

Any advice, or pointers to references would be appreciated.

Harry Hurd

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