Hello Alex, One of our developers had this to say in response to your question:
I believe the ratios in question were generated as a comparison between a tissue (one array) against a median... either that median is the median of all tissues in that tissue category (e.g. five different types of brain tissue), OR the median of all medians of tissue categories for all tissues collected. "Reference" is a better word when describing the basal level of expression expected from cells i.e. the control sample, time-zero, etc... but in the case of the GNF Atlas, all cells are at a basal state and it isn't really possible to pick one type of cell as the typical example of median level expression. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/11/10 5:28 AM, guoshicheng2005 wrote: > Hi Mary: > When i use the application "gene sorter", i want to set "gene sorter > filter" in the part III: > GNF Atlas 2 - GNF Expression Atlas 2 Data from U133A and GNF1H Chips > Note: the values here range from about -5.0 to 5.0. > These are calculated as logBase2(tissue/reference). > > I want to know what the reference is? can you tell me the representation of > this reference! > Thank you very much. Yours help will be great appreciated.Best wishes! > yours sincerely Alex > > > > > -- > > Cancer Epigenetics and Gene Therapy Program, > The State-key Laboratory for Oncogenes and Relatead Genes, > Shanghai Cancer Institute, > Shanghai Jiaotong University, > LN 2200/25, Xietu Road, > Shanghai 200032, China > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
