[BioC] Tools for comparing microarray data on a snp level

[Tim Triche]

How about ggtools?

On Friday, March 19, 2010, Sean Davis <seandavi at gmail.com> wrote:
> On Thu, Mar 18, 2010 at 11:05 AM, Vincent Davis
> <vincent at vincentdavis.net> wrote:
>> First, I am very new to this and have been learning a lot in a 3 week crash
>> course involvement a project. My point is that I am not great with the
>> terminology.
>>
>> What I have, ~50 affycel files, and 3 groups of ~8 samples each for which I
>> know the genome for, ie I know what probes/sequences should bind. We do not
>> have a CDF file as this is a custom array with a mix of probe purposes.
>> Basically these 3 groups of 8 are my means of validating the method used
>>
>> The other ~25 are unknown and I would like a to put a probability on each
>> probe/sequence of the likelihood that a sequence that matches. ie is in the
>> genome. of the unknown.
>>
>> I also have single snp mismatch data for each of the known and the location
>> of the mismatch in the sequence.
>>
>>
>> Are there any tools in bioconductor and or methods that I should look at. Up
>> to this point I have been using python to merge the different data and do
>> some initial analysis.
>
> Hi, Vince.  You might have a look at the affy and oligo packages for
> data import and normalization possibilities.  I have to admit that I'm
> not sure what workflow will be appropriate without a CDF file, though.
>  The limma package (and several others) is good for looking at
> differential hybridization signal.  R is a fantastic tool for data
> exploration, so looking at the effect of snp position and
> presence/absence in your data should be possible with basic plotting
> and hypothesis tests.
>
> Others with more experience in the field of comparative genomics might
> have more detailed thoughts.
>
> Sean
>
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