[BioC] asymmetry in up and down regulation

[Ben Bolstad]

I don't think that this is really a bias. There are probesets that have
been observed to perform much like the "official" spikeins for various
reasons. See

http://affycomp.biostat.jhsph.edu/whymore.html

for details. These probesets would be giving the asymmetry out in the
extremes of the plot you referred to.

Ben


On Mon, 2003-08-11 at 14:47, Chris Paulse wrote:
> Figure 5 in the recent Nucleic Acids Research 2003, Vol. 31, No. 4 e15
> (http://nar.oupjournals.org/cgi/content/full/31/4/e15/GNG015F5) shows an 
> interesting asymmetry in the distribution of fold changes for non-spiked in 
> genes.  Can anyone comment on the reason for this?  Here, dChip has the 
> least amount of bias.
> 
> Thanks,
> Chris
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad