Hi all- I am fairly new to bioconductor and am very excited about the example described in the affycoretools vignette since 1) it would make my mentor very happy (almost the exact situation that we have in the data set), 2) seemed like a simple solution to a issue I was not sure how to approach and 3) package seemed straightforward and easy to use. This is probably a stupid question arising from the fact that I have yet to fully understand R and bioconductor but I have tried to spend a better portion of the day trying to figure where I am going wrong and having no luck. I am trying to compare samples (two treatment groups) amplified two different ways and see which differentially expressed genes are shared between the two different methodologies. According to the PCA plot I need to compute the expression values for each methodology separately and then combine the data. I can not seem to create the new expression set properly to perform the limma analysis. I have attached a text file with my R code. If anyone could point me in the right direction (either the mistake I am makeing or even the vignette that I should read closer) I would appreciate the help. Sorry if this seems very silly but we do not have anyone here familiar with Bioconductor to go to for help. Thanks Louisa (See attached file: affycoretoolsJune232008.txt) "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu

Hi Louisa, Louisa A Rispoli/AS/EXP/UTIA wrote: > Hi all- > > I am fairly new to bioconductor and am very excited about the example > described in the affycoretools vignette since 1) it would make my mentor > very happy (almost the exact situation that we have in the data set), 2) > seemed like a simple solution to a issue I was not sure how to approach and > 3) package seemed straightforward and easy to use. This is probably a > stupid question arising from the fact that I have yet to fully understand R > and bioconductor but I have tried to spend a better portion of the day > trying to figure where I am going wrong and having no luck. I am trying to > compare samples (two treatment groups) amplified two different ways and > see which differentially expressed genes are shared between the two > different methodologies. According to the PCA plot I need to compute the > expression values for each methodology separately and then combine the > data. I can not seem to create the new expression set properly to perform > the limma analysis. I have attached a text file with my R code. As I am sure you have noticed by now, most attachments are stripped before being sent on to the list. A better approach would be to either put your code inline, or better yet, try to simplify your code as much as possible and then just give the simplified code. Best, Jim > > If anyone could point me in the right direction (either the mistake I am > makeing or even the vignette that I should read closer) I would appreciate > the help. Sorry if this seems very silly but we do not have anyone here > familiar with Bioconductor to go to for help. > > Thanks > > Louisa > > (See attached file: affycoretoolsJune232008.txt) > > "If we knew what we were doing, it wouldn't be called Research." - Albert > Einstein > > Louisa Rispoli, Ph.D. Reproductive Physiology > Department of Animal Science > University of Tennessee, Knoxville > A105 Johnson Animal Research and Teaching Unit > 1750 Alcoa Highway > Knoxville, TN 37920 > phone:(865) 946-1874 > fax:(865) 946-1010 > email: lrispoli at utk.edu > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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