Hi All, I am new to Microarray Analysis and this list. I posted this before, I don't know if it was posted correctly. I want to analyze just one chip..........Is limma suitable for this? Could you suggest any other package. Thank you very much. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

Khan, Sohail wrote: > Hi All, > > I am new to Microarray Analysis and this list. I posted this before, I don't know if it was posted correctly. > I want to analyze just one chip..........Is limma suitable for this? Could you suggest any other package. > Thank you very much. Your previous question was posted correctly. Unfortunately there is no package for the analysis of a single chip (especially if you are talking about an Affy chip...). With a single cDNA chip, all you can do is normalize the cy5 and cy3 values, compute the log ratios, and then look for genes that have a value larger (in absolute terms) than some cutoff (the traditional cutoff being 2-fold). You could certainly use limma for the intra-chip normalization, but at that point I think you are done. If you are using an Affy chip, you should note that the expression measures are *relative* values, and are meaningless without something to compare to. Best, Jim > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Your mail got through. One way to check this yourself is to check the BioConductor mailing archives at https://stat.ethz.ch/pipermail/bioconductor/ I do not think you can do much with one chip. Perhaps some image analysis problems etc. But even if you can do some "analysis" on a single chip, what will it tell you ? You will not be able to separate biological from technical variation. If you had some duplicated spots on the chip then perhaps hope to estimate technical variation. Please give us a more information on your study design and objectives. Regards, Adai On Thu, 2005-03-10 at 15:19 -0500, Khan, Sohail wrote: > Hi All, > > I am new to Microarray Analysis and this list. I posted this before, I don't know if it was posted correctly. > I want to analyze just one chip..........Is limma suitable for this? Could you suggest any other package. > Thank you very much. > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >