[BioC] gcrma on PM-only Affy data

[Jenny Drnevich]

Hi Jean,

I'm in a similar situation where I'd like to use gcrma on a PM-only custom 
Affy chip. How many NCprobes are needed to get a good estimate of the 
relationship between background and probe sequence? My clients didn't 
spike-in the polyA controls, but there are only 24 probesets X 11 = 264 
probes in all for the polyA controls. This seems like not enough to get a 
good estimate...  I'm trying to find out if any other negative controls 
were put on the array, but if not, do you have any other suggestions?

Thanks,
Jenny


At 11:17 AM 10/25/2006, Zhijin (Jean) Wu wrote:
>Hi, Karen,
>You can choose type "affinities" in bg.adjust.gcrma.
>You will also need to specify which probes you would consider as negative
>controls ("NCprobes") in order to estimate the relationship between
>background and probe sequences. If, in your experiment, only a small 
>fraction of probes
>are expected to have specific target (for example, only a small fraction of
>genes are expressed), you can use all PM probes as NCprobes if there's
>no other choice.
>
>bg.adjust.gcrma(object, NCprobe=
>index.of.your.control.probes,type="affinities")
>
>Is the hybridization method the same as what's used for standard
>GeneChip arrays? If not, you may want to estimate the object
>"affinity.info" using your own data instead of the default. In this case
>you will either need negative control probes or run an negative control
>experiment.
>
>Jean Wu
>
>On Wed, 25 Oct 2006, Karen Vranizan wrote:
>
> > I have a PM-only Affy chip.  Is it possible to do gcrma on this 
> data?  Thank you.
> >
> > Karen Vranizan
> > Functional Genomics Lab
> > 261A Life Sciences Addition
> > Mail Code #3200
> > UC Berkeley, CA 94720-3200
> >
> > Phone: 510-642-7520
> > Fax:      510-643-2685
> > email: vranizan at berkeley.edu
> >
> >       [[alternative HTML version deleted]]
> >
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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e-mail: drnevich at uiuc.edu