[BioC] Tools for comparing microarray data on a snp level
seandavi at gmail.com
Fri Mar 19 13:16:43 CET 2010
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
> 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.
More information about the Bioconductor