[BioC] altcdfenvs: mapping probes and creating new probe sets: guidance requested

[James W. MacDonald]

Hi Ariel,

On 6/28/2011 7:23 PM, Ariel Grostern wrote:
>
>
> Hello,
>
> I am using R 2.10.0. The sessionInfo data is below at the end
> of this message. I am using Ubuntu 10.04.

No it isn't, as you are sending HTML to a text-only listserv and getting 
things chopped off. Please switch to text when sending.

Best,

Jim


>
> I am attempting to re-annotate
> custom Affy PM-only chip using a new gene-annotation for my prokaryotic
> genome. I have gotten stuck on altcdfenvs, however.
>
> What I have done so
> far:
>
> 1. Changed the makeProbePackage code to not require MM probe data
>
>
> 2. Created a probe package from my probe_tab file with makeProbePackage
> (for some reason 4800 probes did not match between the probe_tab file and
> the Affy-supplied .CDF file)
>
> 3. Installed the new probe package with help
> from James MacDonald
>
> 4. Started following the altcdfenvs
> documentation....selected the constituting elemets, matched the probes....
> Everything went smoothly until match analysis:
>
>> alt.cdf
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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