[BioC] gcrma on PM-only Affy data

[Zhijin (Jean) Wu]

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
>
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