[BioC] appyPLM residual plots: any hint?

[Ben Bolstad]

Spend some time comparing your images to these (particularly some of the
full dataset images):

http://www.stat.berkeley.edu/~bolstad/PLMImageGallery/index.html

Also make sure you look at the the NUSE and RLE plots (boxplot() and
Mbox() in affyPLM) these will help you decide if any of the chips are
discordant.

Thanks,

Ben






On Tue, 2004-10-12 at 04:56, Stefano Calza wrote:
> Hi.
> 
> I'm using affyPLM models to check for some array quality. Here you can see the plots of the residuals
> 
> www.med.unibs.it/dip/dip_SBB/sez_statist/calza/bioinfo
> 
> So, afaik some of those chip look a bit suspicious to, i.e. LptMOE8 and LptMOE9 and also LptMOE11 and LptMOE12. How should I interpret those 
> "stains"? Are this array that bad? Is it reasonable to exclude those probes from the analyses (and is it possible)?
> 
> TIA,
> Stefano
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad