In a a sense tiling arrays are more general tools than expression arrays. What you are looking for (and hence your method of analysis) is (or at least should be) dependent on your research question. In comparison, with an expression array you are interested in genes that are DE between different experimental conditions. /Kasper On Jan 26, 2006, at 1:36 AM, Dario Greco wrote: > hi all, > we are probably going to use affymetrix tiling arrays for human. > i have understood that in some ways it is possible to use gcrma for > image > preprocessing and that the quantile normalization might be a > reasonable > method. > but i was wondering if there is (or if there is going to be) any ad > hoc tool > in bioconductor also for the later steps of the analysis and > interpretations > of such experiments. > any suggestions are warmly appreciated. > thanks, > > greetings > d > > -- > > Dario Greco > > Institute of Biotechnology - University of Helsinki > Building Cultivator II > P.O.Box 56 Viikinkaari 4 > FIN-00014 Finland > > Office: +358 9 191 58951 > Fax: +358 9 191 58952 > Mobile: +358 44 023 5780 > > Lab WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/ > > Personal WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Dario, I'll second this opinion. The design of the array, hypotheses being tested, sample characteristics, genomic features and how they relate to the features on the array, experimental design, and tiling array technology all play a VERY LARGE part in defining what can and should be done in terms of normalization and analysis. I'm not sure that relying on any "canned" solution for tiling arrays is possible at this time given the diverse nature of experiments that can be performed with them. Sean On 2/1/06 12:35 AM, "Kasper Daniel Hansen" <khansen at="" stat.berkeley.edu=""> wrote: > In a a sense tiling arrays are more general tools than expression > arrays. What you are looking for (and hence your method of analysis) > is (or at least should be) dependent on your research question. In > comparison, with an expression array you are interested in genes that > are DE between different experimental conditions. > > /Kasper > > On Jan 26, 2006, at 1:36 AM, Dario Greco wrote: > >> hi all, >> we are probably going to use affymetrix tiling arrays for human. >> i have understood that in some ways it is possible to use gcrma for >> image >> preprocessing and that the quantile normalization might be a >> reasonable >> method. >> but i was wondering if there is (or if there is going to be) any ad >> hoc tool >> in bioconductor also for the later steps of the analysis and >> interpretations >> of such experiments. >> any suggestions are warmly appreciated. >> thanks, >> >> greetings >> d >> >> -- >> >> Dario Greco >> >> Institute of Biotechnology - University of Helsinki >> Building Cultivator II >> P.O.Box 56 Viikinkaari 4 >> FIN-00014 Finland >> >> Office: +358 9 191 58951 >> Fax: +358 9 191 58952 >> Mobile: +358 44 023 5780 >> >> Lab WebPage: >> http://www.biocenter.helsinki.fi/bi/dna-microarray/ >> >> Personal WebPage: >> http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

hello, thanks a lot for your messages. actually, in case we will approach to the tiling arrays, we would like to screen the transcriptome, and not the genome. we would actually like to find non coding (novel ?!?!) RNAs having a different expresison pattern in several samples...or at least this would be the ultimate dream! so, in this situation, what would be the best analytical approach, in your opinion? thanks again, yours d -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna- microarray/dario.htm Quoting Sean Davis <sdavis2 at="" mail.nih.gov="">: > Dario, > > I'll second this opinion. The design of the array, hypotheses being > tested, > sample characteristics, genomic features and how they relate to the > features > on the array, experimental design, and tiling array technology all play > a > VERY LARGE part in defining what can and should be done in terms of > normalization and analysis. I'm not sure that relying on any "canned" > solution for tiling arrays is possible at this time given the diverse > nature > of experiments that can be performed with them. > > Sean > > On 2/1/06 12:35 AM, "Kasper Daniel Hansen" <khansen at="" stat.berkeley.edu=""> > wrote: > > > In a a sense tiling arrays are more general tools than expression > > arrays. What you are looking for (and hence your method of analysis) > > is (or at least should be) dependent on your research question. In > > comparison, with an expression array you are interested in genes that > > are DE between different experimental conditions. > > > > /Kasper > > > > On Jan 26, 2006, at 1:36 AM, Dario Greco wrote: > > > >> hi all, > >> we are probably going to use affymetrix tiling arrays for human. > >> i have understood that in some ways it is possible to use gcrma for > >> image > >> preprocessing and that the quantile normalization might be a > >> reasonable > >> method. > >> but i was wondering if there is (or if there is going to be) any ad > >> hoc tool > >> in bioconductor also for the later steps of the analysis and > >> interpretations > >> of such experiments. > >> any suggestions are warmly appreciated. > >> thanks, > >> > >> greetings > >> d > >> > >> -- > >> > >> Dario Greco > >> > >> Institute of Biotechnology - University of Helsinki > >> Building Cultivator II > >> P.O.Box 56 Viikinkaari 4 > >> FIN-00014 Finland > >> > >> Office: +358 9 191 58951 > >> Fax: +358 9 191 58952 > >> Mobile: +358 44 023 5780 > >> > >> Lab WebPage: > >> http://www.biocenter.helsinki.fi/bi/dna-microarray/ > >> > >> Personal WebPage: > >> http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >