Question: Agilent's duplicate spots
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12.5 years ago by
Mcmahon, Wyatt50 wrote:
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ADD COMMENTlink modified 12.5 years ago by Naomi Altman6.0k • written 12.5 years ago by Mcmahon, Wyatt50
Answer: Agilent's duplicate spots
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gravatar for Francois Pepin
12.5 years ago by
Francois Pepin1.3k
Francois Pepin1.3k wrote:
Hi Wyatt, I don't think it is possible to do that. Moreover, only a few probes are actually replicated on the array. You can look at them as internal control for consistency. In our experience, the intensities for all those spots are extremely close. We actually end up ignoring all but one of them because they are equivalent. It would also be reasonable for to just average them. Those are very different from the genes that have several probes representing them. We tend to see large differences between the expression of those probes and I would not average them or take an arbitrary probe to represent the whole gene. If I didn't understand your question properly, you might want to give us some more information about the chip and the probes you're talking about. Francois On Thu, 2007-06-07 at 13:16 -0500, Mcmahon, Wyatt wrote: > Hello everyone, > > > > I'm new to bioconductor and microarray in general, so please excuse my > ignorance. > > > > I am trying to analyze my microarray experiment using limma. We have > used Agilent to spot our arrays, and we have duplicate spots. However, > these spots are placed randomly over the entire chip. How do I let > limma know that there are duplicate spots with a random distribution. I > can't seem to find anything that explains this. > > > > Thanks in advance, > > > > Wyatt > > > > K. Wyatt McMahon, Ph.D. > > Postdoctoral Research Associate - Functional Genomics Center and > Services Facility > > Texas Tech University > > Department of Plant and Soil Sciences > > Campus Box 42122 > > 79409 > > 806-742-5073 ext. 263 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
ADD COMMENTlink written 12.5 years ago by Francois Pepin1.3k
Answer: Agilent's duplicate spots
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gravatar for Naomi Altman
12.5 years ago by
Naomi Altman6.0k
Naomi Altman6.0k wrote:
I think most of us have found that the spatial aspect is not that important. Normalize the data and then sort by gene so that the duplicates are adjacent in the data matrix. --Naomi At 02:16 PM 6/7/2007, Mcmahon, Wyatt wrote: >Hello everyone, > > > >I'm new to bioconductor and microarray in general, so please excuse my >ignorance. > > > >I am trying to analyze my microarray experiment using limma. We have >used Agilent to spot our arrays, and we have duplicate spots. However, >these spots are placed randomly over the entire chip. How do I let >limma know that there are duplicate spots with a random distribution. I >can't seem to find anything that explains this. > > > >Thanks in advance, > > > >Wyatt > > > >K. Wyatt McMahon, Ph.D. > >Postdoctoral Research Associate - Functional Genomics Center and >Services Facility > >Texas Tech University > >Department of Plant and Soil Sciences > >Campus Box 42122 > >79409 > >806-742-5073 ext. 263 > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
ADD COMMENTlink written 12.5 years ago by Naomi Altman6.0k
Thank you very much, Naomi! When you say, "sort by gene so that the duplicates are adjacent in the data matrix," do you mean by using Excel? Thanks, Wyatt -----Original Message----- From: Naomi Altman [mailto:naomi@stat.psu.edu] Sent: Thursday, June 07, 2007 3:36 PM To: Mcmahon, Wyatt; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Agilent's duplicate spots I think most of us have found that the spatial aspect is not that important. Normalize the data and then sort by gene so that the duplicates are adjacent in the data matrix. --Naomi At 02:16 PM 6/7/2007, Mcmahon, Wyatt wrote: >Hello everyone, > > > >I'm new to bioconductor and microarray in general, so please excuse my >ignorance. > > > >I am trying to analyze my microarray experiment using limma. We have >used Agilent to spot our arrays, and we have duplicate spots. However, >these spots are placed randomly over the entire chip. How do I let >limma know that there are duplicate spots with a random distribution. I >can't seem to find anything that explains this. > > > >Thanks in advance, > > > >Wyatt > > > >K. Wyatt McMahon, Ph.D. > >Postdoctoral Research Associate - Functional Genomics Center and >Services Facility > >Texas Tech University > >Department of Plant and Soil Sciences > >Campus Box 42122 > >79409 > >806-742-5073 ext. 263 > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
ADD REPLYlink written 12.5 years ago by Mcmahon, Wyatt50
Hi Wyatt, Mcmahon, Wyatt wrote: > Thank you very much, Naomi! > > When you say, "sort by gene so that the duplicates are adjacent in the > data matrix," do you mean by using Excel? That's a joke, right? If not, you need to sit down and read 'An Introduction to R'. Right now. Really. You could sort using Excel, but that would be like using the butt-end of a screwdriver to pound a nail when you have a hammer hanging on your belt. You could do it, and eventually you would get the job done, but you are really using the wrong tool for the job. Best, Jim > > Thanks, > > Wyatt > > -----Original Message----- > From: Naomi Altman [mailto:naomi at stat.psu.edu] > Sent: Thursday, June 07, 2007 3:36 PM > To: Mcmahon, Wyatt; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Agilent's duplicate spots > > I think most of us have found that the spatial aspect is not that > important. Normalize the data and then sort by gene so that the > duplicates are adjacent in the data matrix. > > --Naomi > > At 02:16 PM 6/7/2007, Mcmahon, Wyatt wrote: > >>Hello everyone, >> >> >> >>I'm new to bioconductor and microarray in general, so please excuse my >>ignorance. >> >> >> >>I am trying to analyze my microarray experiment using limma. We have >>used Agilent to spot our arrays, and we have duplicate spots. However, >>these spots are placed randomly over the entire chip. How do I let >>limma know that there are duplicate spots with a random distribution. > > I > >>can't seem to find anything that explains this. >> >> >> >>Thanks in advance, >> >> >> >>Wyatt >> >> >> >>K. Wyatt McMahon, Ph.D. >> >>Postdoctoral Research Associate - Functional Genomics Center and >>Services Facility >> >>Texas Tech University >> >>Department of Plant and Soil Sciences >> >>Campus Box 42122 >> >>79409 >> >>806-742-5073 ext. 263 >> >> >> >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>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 > > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.5 years ago by James W. MacDonald52k
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