Question: combining hgu133a and hgu133b
0
gravatar for Mayte Suarez-Farinas
7.6 years ago by
United States
Mayte Suarez-Farinas510 wrote:
Hi all, I have HGU133a , HGU133b chips done in the same set of samples. Additionally I have hgu133plus2 chips in a different set of samples. Since "a+b" is almost "plus2", is tehre a way to combinethose two affybatchs ? Any guidance will be appreciated!! Mayte Suarez-Farinas Research Assistant Professor, Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178, New York, NY, 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232
hgu133a hgu133b hgu133plus2 • 787 views
ADD COMMENTlink modified 7.6 years ago • written 7.6 years ago by Mayte Suarez-Farinas510
Answer: combining hgu133a and hgu133b
0
gravatar for Mayte Suarez-Farinas
7.6 years ago by
United States
Mayte Suarez-Farinas510 wrote:
Hi all, I have HGU133a , HGU133b chips done in the same set of samples. Additionally I have hgu133plus2 chips in a different set of samples. Since "a+b" is almost "plus2", is tehre a way to combinethose two affybatchs ? Any guidance will be appreciated!! Mayte Suarez-Farinas Research Assistant Professor, Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178, New York, NY, 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232
ADD COMMENTlink written 7.6 years ago by Mayte Suarez-Farinas510
Hi Mayte, The short answer is no. You could hypothetically create a mixture cdf that only contains probesets that are in the intersection of these three chip types and then normalize. Ben Bolstad has a page containing mixture cdfs for some arrays (http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html) but he never to my knowledge made one for the arrays you have. In general, I think you would be better off to normalize separately and then combine. Best, Jim On 4/27/2012 4:27 PM, Mayte Suarez-Farinas wrote: > Hi all, > > I have HGU133a , HGU133b chips done in the same set of samples. Additionally I have hgu133plus2 chips in a different set of samples. > Since "a+b" is almost "plus2", is tehre a way to combinethose two affybatchs ? > > Any guidance will be appreciated!! > > > > Mayte Suarez-Farinas > Research Assistant Professor, Laboratory of Investigative Dermatology > Biostatistician, Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178, > New York, NY, 10065 > Phone: +1(212) 327-8213 > Fax: +1(212) 327-8232 > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 7.6 years ago by James W. MacDonald51k
Hi, On Fri, Apr 27, 2012 at 4:51 PM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Mayte, > > The short answer is no. > > You could hypothetically create a mixture cdf that only contains probesets > that are in the intersection of these three chip types and then normalize. > Ben Bolstad has a page containing mixture cdfs for some arrays > (http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html) but he never to my > knowledge made one for the arrays you have. > > In general, I think you would be better off to normalize separately and then > combine. Wouldn't another approach be to use one of them there meta-analysis type approaches, such as: http://www.bioconductor.org/packages/2.10/bioc/html/RankProd.html or http://www.bioconductor.org/packages/2.10/bioc/html/metaArray.html or? Never used them myself, but my mental note for these packages was there for when I wanted to tackle such a situation (notes can be wrong, of course -- mental ones, even more so since no ink was actually invested). -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
ADD REPLYlink written 7.6 years ago by Steve Lianoglou12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 302 users visited in the last hour