R help - Jun 2012 - Can someone recommend a package for SNP cluster analysis of Fluidigm microarrays?

I know that there are quite a few packages out that there for cluster
analysis.  The problem that I am facing is finding a package that will not
incorporate all my samples into clusters but just the samples that fit a
threshold (that I have not set yet and may need help finding the right
level) for genotyping. It should be able to "no call" samples outside
the
clusters. It also needs to accommodate a negative control sample by not
including it in any genotype cluster.

I'm looking at both nuclear and mitochondrial DNA so hopefully it can be
sophisticated enough to set the number of cluster between two or three
within the array.

These genotyping arrays are either 48 samples x 48 assays, 96x96, or 192x24
and it would be nice if it could accommodate any range of samples and
assays.

the data headings from the csv are:

ID,Assay,Allele Y,Allele X,Name,Type,Auto,Confidence,Final,Converted,Allele
Y,Allele X

where Allele Y and Allele X are the plotted values and the vectors within
the data.frame are 9216 (96x96) long.

So what would be the recommended package for moving to a more quantifiable
method of genotyping using cluster analysis?

Thanks again.  Forgive me if this is a better question for bioconductor.  I
will provide any additional context that I might have forgot to add here
that could help.

	[[alternative HTML version deleted]]

I do think this is more of a Bioconductor question -- but no worries,
they're all much nicer there than we are here and won't flame you if
you double post :-)

Best,
Michael

On Thu, Jun 14, 2012 at 12:37 PM, Hans Thompson
<hans.thompson1 at gmail.com> wrote:
> I know that there are quite a few packages out that there for cluster
> analysis. ?The problem that I am facing is finding a package that will not
> incorporate all my samples into clusters but just the samples that fit a
> threshold (that I have not set yet and may need help finding the right
> level) for genotyping. It should be able to "no call" samples
outside the
> clusters. It also needs to accommodate a negative control sample by not
> including it in any genotype cluster.
>
> I'm looking at both nuclear and mitochondrial DNA so hopefully it can
be
> sophisticated enough to set the number of cluster between two or three
> within the array.
>
> These genotyping arrays are either 48 samples x 48 assays, 96x96, or 192x24
> and it would be nice if it could accommodate any range of samples and
> assays.
>
> the data headings from the csv are:
>
> ID,Assay,Allele Y,Allele X,Name,Type,Auto,Confidence,Final,Converted,Allele
> Y,Allele X
>
> where Allele Y and Allele X are the plotted values and the vectors within
> the data.frame are 9216 (96x96) long.
>
> So what would be the recommended package for moving to a more quantifiable
> method of genotyping using cluster analysis?
>
> Thanks again. ?Forgive me if this is a better question for bioconductor. ?I
> will provide any additional context that I might have forgot to add here
> that could help.
>
> ? ? ? ?[[alternative HTML version deleted]]
>
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