Identifying the genome sequence of an affy probe

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Schragi Schwartz ▴ 20

@schragi-schwartz-4932

Last seen 10.3 years ago

Hi, I'm looking for a package that will give me the sequence of affy probes in the Human?U133A 2.0 package. In other words, I have a list of affy ids (e.g. 237488_s_at, etc.) and I would like to know the sequences of original 25 mers this probe corresponds to. Thanks, Schragi

probe affy probe affy • 860 views

ADD COMMENT • link updated 13.2 years ago by James W. MacDonald 67k • written 13.2 years ago by Schragi Schwartz ▴ 20

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Hi, On Thu, Oct 27, 2011 at 11:54 AM, Schragi Schwartz <schwartz at="" broadinstitute.org=""> wrote: > Hi, > > I'm looking for a package that will give me the sequence of affy > probes in the Human?U133A 2.0 package. In other words, I have a list > of affy ids (e.g. 237488_s_at, etc.) and I would like to know the > sequences of original 25 mers this probe corresponds to. Try: http://www.bioconductor.org/packages/release/data/annotation/html/hgu1 33a2probe.html -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 18 months ago

United States

The easiest thing is to use the hgu133a2probe package, if all you want is the sequences. Be careful about your terminology though. 237488_s_at is a _probeset_ consisting of 11-16 probes (depending which array, I think the array you are interested in has 11 probes per probeset). So you will get 11 sequences. Kasper On Thu, Oct 27, 2011 at 11:54 AM, Schragi Schwartz <schwartz at="" broadinstitute.org=""> wrote: > Hi, > > I'm looking for a package that will give me the sequence of affy > probes in the Human?U133A 2.0 package. In other words, I have a list > of affy ids (e.g. 237488_s_at, etc.) and I would like to know the > sequences of original 25 mers this probe corresponds to. > > Thanks, > Schragi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 13.2 years ago Kasper Daniel Hansen ★ 6.5k

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 hours ago

United States

Hi Schragi, You want the hgu133a2probe package. Best, Jim On 10/27/2011 11:54 AM, Schragi Schwartz wrote: > Hi, > > I'm looking for a package that will give me the sequence of affy > probes in the Human U133A 2.0 package. In other words, I have a list > of affy ids (e.g. 237488_s_at, etc.) and I would like to know the > sequences of original 25 mers this probe corresponds to. > > Thanks, > Schragi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD COMMENT • link 13.2 years ago James W. MacDonald 67k

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Thank you very much! On Thu, Oct 27, 2011 at 12:06 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Schragi, > > You want the hgu133a2probe package. > > Best, > > Jim > > > > On 10/27/2011 11:54 AM, Schragi Schwartz wrote: >> >> Hi, >> >> I'm looking for a package that will give me the sequence of affy >> probes in the Human U133A 2.0 package. In other words, I have a list >> of affy ids (e.g. 237488_s_at, etc.) and I would like to know the >> sequences of original 25 mers this probe corresponds to. >> >> Thanks, >> Schragi >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >

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