Tools for comparing microarray data on a snp level

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Vincent Davis ▴ 40

@vincent-davis-3969

Last seen 10.6 years ago

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. *Vincent Davis 720-301-3003 * vincent@vincentdavis.net my blog <http: vincentdavis.net=""> | LinkedIn<http: www.linkedin.com="" in="" vincentdavis=""> [[alternative HTML version deleted]]

SNP cdf SNP cdf • 836 views

ADD COMMENT • link updated 15.1 years ago by Sean Davis 21k • written 15.1 years ago by Vincent Davis ▴ 40

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Sean Davis 21k

@sean-davis-490

Last seen 8 weeks ago

United States

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

ADD COMMENT • link 15.1 years ago Sean Davis 21k

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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann

ADD REPLY • link 15.1 years ago Tim Triche ★ 4.2k

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