Dear Dott. Friedman, I TOTALLY AGREE with you!! I stressed the people gave me the data to do at least 3 replicates per condition but samples are not available anymore, unfortunately.. Best E. Richard Friedman (friedman at cancercenter.columbia.edu) wrote: > > Dear Eleonora, > > The results will not be reliable because you will not > take the variability (both biological and technical) into account. > One replicate each will only give you log Foldchanges, but no > measure of the variability. Whether you go ahead or not > is up to you but I try to avoid doing this whenever possible > and I also tell the people that any such results come with > a big question mark. > > with hope that this helps, > Rich > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In memoriam, Ray Bradbury > > On Sep 10, 2012, at 2:38 PM, Eleonora Lusito wrote: > > > Dear BioC users, I have a question regarding microarray data analysis (Human > > Affymetrix one color). My point is that I have just 1 sample TREATMENT and 1 > > sample REFERENCE. Neither technical replicates nor biological replicates are > > available. A statistical test to find differentially expressed genes between > > the two conditions seems to me impossible (even the simple t-test) due to the > > absence of replicates. People who asked me to do the analysis were interested > > only in finding the genes changing between the two conditions. In this > > conditions, in my opinion only the fold change is possible just to give a > > general view of the behavior of the genes. Any other suggestion about this > > issue? > > > > Thanks a lot > > > > E. > > > > -- > > Eleonora Lusito > > Computational Biology PhD student > > Molecular Medicine Program > > via Ripamonti 435, 20141 Milano, Italy > > > > Phone number: +390294375160 > > e-mail: eleonora.lusito at ieo.eu > > > > _______________________________________________ > > 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 > > -- Eleonora Lusito Computational Biology PhD student Molecular Medicine Program via Ripamonti 435, 20141 Milano, Italy Phone number: +390294375160 e-mail: eleonora.lusito at ieo.eu

Hi Tom, thanks a lot for your suggestions! I'll ask them for a marker! Thanks again Best E. Thomas H. Hampton (Thomas.H.Hampton at dartmouth.edu) wrote: > > This is a great question. Obviously, with an N of 1, you are sorely limited in what > you can say. In your consideration, you need to consider the ratio between your > two samples, but you should also consider whether the ratio is based on a gene > that is well-expressed in your system. Most genes are not very well expressed, > and so many of your "largest" ratios will involve genes that are expressed at very > low levels -- low enough so you might wonder whether the ratio is just pure > noise. If I were you, I would look first at genes that are well expressed and show a large > ratio, as well. You may also want to place emphasis on genes that are well understood > and well annotated. At the end of the day, you can only make very preliminary statements > of course, but you may see something that is worth following up on... > > Best > > Tom > On Sep 10, 2012, at 2:38 PM, Eleonora Lusito wrote: > > > Dear BioC users, I have a question regarding microarray data analysis (Human > > Affymetrix one color). My point is that I have just 1 sample TREATMENT and 1 > > sample REFERENCE. Neither technical replicates nor biological replicates are > > available. A statistical test to find differentially expressed genes between > > the two conditions seems to me impossible (even the simple t-test) due to the > > absence of replicates. People who asked me to do the analysis were interested > > only in finding the genes changing between the two conditions. In this > > conditions, in my opinion only the fold change is possible just to give a > > general view of the behavior of the genes. Any other suggestion about this > > issue? > > > > Thanks a lot > > > > E. > > > > -- > > Eleonora Lusito > > Computational Biology PhD student > > Molecular Medicine Program > > via Ripamonti 435, 20141 Milano, Italy > > > > Phone number: +390294375160 > > e-mail: eleonora.lusito at ieo.eu > > > > _______________________________________________ > > 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 > > > > > -- Eleonora Lusito Computational Biology PhD student Molecular Medicine Program via Ripamonti 435, 20141 Milano, Italy Phone number: +390294375160 e-mail: eleonora.lusito at ieo.eu