[BioC] appyPLM residual plots: any hint?

[Fangxin Hong]

I am sorry it may sound silly. But I can't find useful information about
affyPLM package in bioconductor site. It seems useful to check array
quality for some artifac. Anyone can refer me to documentation of this
package.

Thanks a lot!

fangxin

> 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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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> --
> Ben Bolstad <bolstad at stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
>
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>
>


-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu