help with affy st gene arrays
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Yongde Bao ▴ 170
@yongde-bao-244
Last seen 10.2 years ago
Dear BioConductor experts, I wonder if anyone would be generous enough to share some scripts/screen images they use to analyze Affy ST gene arrays, either for human or mouse. I am particularly interested in learning what packages they use and what the output files look like. Thanks much, Yongde Dept. Microbiology University of Virginia
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@achilleas-pitsillides-4316
Last seen 10.2 years ago
Hi Yongde, I am no expert but for the last Human Gene 1.0 ST array data I analyzed I used the xps package for pre-processing and then to assess differential expression I used the limma package. I am sorry I don't have any screenshots but both packages have nice documentation in their vignettes, which should be really straight forward to follow. cheers, Achilleas On Thu, Nov 11, 2010 at 3:46 PM, YBao <yb8d@virginia.edu> wrote: > Dear BioConductor experts, > > > I wonder if anyone would be generous enough to share some > scripts/screen images they use to analyze Affy ST gene arrays, either > for human or mouse. I am particularly interested in learning what > packages they use and what the output files look like. > > Thanks much, > > > > Yongde > > Dept. Microbiology > University of Virginia > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thanks so much, Achilleas, for the quick response. I will try to use those two packages and see how far I can go with them. Yongde On Thu, Nov 11, 2010 at 4:24 PM, Achilleas Pitsillides <anp4r at="" virginia.edu=""> wrote: > Hi Yongde, > > I am no expert but for the last? Human Gene 1.0 ST array data I analyzed I > used the xps package for pre-processing and then to assess differential > expression I used the limma package. I am sorry I don't have any screenshots > but both packages have nice documentation in their vignettes, which should > be really straight forward to follow. > > cheers, > Achilleas > > > > On Thu, Nov 11, 2010 at 3:46 PM, YBao <yb8d at="" virginia.edu=""> wrote: >> >> Dear BioConductor experts, >> >> >> I wonder if anyone would be generous enough to share some >> scripts/screen images they use to analyze Affy ST gene arrays, either >> for human or mouse. I am particularly interested in learning what >> packages they use and what the output files look like. >> >> Thanks much, >> >> >> >> Yongde >> >> Dept. Microbiology >> University of Virginia >> >> _______________________________________________ >> 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 > >
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Hi Yongde, also take a look at the oligo package for normalizing your Gene ST arrays cheers, Mark On 12/11/2010, at 8:51 AM, YBao wrote: > Thanks so much, Achilleas, for the quick response. I will try to use > those two packages and see how far I can go with them. > > Yongde > > On Thu, Nov 11, 2010 at 4:24 PM, Achilleas Pitsillides > <anp4r at="" virginia.edu=""> wrote: >> Hi Yongde, >> >> I am no expert but for the last Human Gene 1.0 ST array data I analyzed I >> used the xps package for pre-processing and then to assess differential >> expression I used the limma package. I am sorry I don't have any screenshots >> but both packages have nice documentation in their vignettes, which should >> be really straight forward to follow. >> >> cheers, >> Achilleas >> >> >> >> On Thu, Nov 11, 2010 at 3:46 PM, YBao <yb8d at="" virginia.edu=""> wrote: >>> >>> Dear BioConductor experts, >>> >>> >>> I wonder if anyone would be generous enough to share some >>> scripts/screen images they use to analyze Affy ST gene arrays, either >>> for human or mouse. I am particularly interested in learning what >>> packages they use and what the output files look like. >>> >>> Thanks much, >>> >>> >>> >>> Yongde >>> >>> Dept. Microbiology >>> University of Virginia >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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
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http://www.bioconductor.org/help/workflows/oligo-arrays/ gives a reasonably thorough discussion of relevant resources On Thu, Nov 11, 2010 at 7:02 PM, Mark Cowley <m.cowley at="" garvan.org.au=""> wrote: > Hi Yongde, > also take a look at the oligo package for normalizing your Gene ST arrays > cheers, > Mark > On 12/11/2010, at 8:51 AM, YBao wrote: > >> Thanks so much, Achilleas, for the quick response. I will try to use >> those two packages and see how far I can go with them. >> >> Yongde >> >> On Thu, Nov 11, 2010 at 4:24 PM, Achilleas Pitsillides >> <anp4r at="" virginia.edu=""> wrote: >>> Hi Yongde, >>> >>> I am no expert but for the last ?Human Gene 1.0 ST array data I analyzed I >>> used the xps package for pre-processing and then to assess differential >>> expression I used the limma package. I am sorry I don't have any screenshots >>> but both packages have nice documentation in their vignettes, which should >>> be really straight forward to follow. >>> >>> cheers, >>> Achilleas >>> >>> >>> >>> On Thu, Nov 11, 2010 at 3:46 PM, YBao <yb8d at="" virginia.edu=""> wrote: >>>> >>>> Dear BioConductor experts, >>>> >>>> >>>> I wonder if anyone would be generous enough to share some >>>> scripts/screen images they use to analyze Affy ST gene arrays, either >>>> for human or mouse. I am particularly interested in learning what >>>> packages they use and what the output files look like. >>>> >>>> Thanks much, >>>> >>>> >>>> >>>> Yongde >>>> >>>> Dept. Microbiology >>>> University of Virginia >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 >
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