Hi, I'm confused about the nature of the data used in the ALL example in Bioconductor. The paper (Chiaretti et al 2004) describes a study of T-cell ALL and doesn't mention BCR-ABL, while the Bioconductor example (e.g. in the Genome Biology paper) works through a comparison of BCR/ABL v. ALL1/AF4, which are, I think, markers for B-ALL. I can't find anything in the phenoData which describes which patients have T-ALL or B-ALL. Thanks. Tom Elliott

The data set has both, library("ALL") data(ALL) ALL$BT ALL$mol.biol... and of course, there is always a man page, ?ALL which if read may help reveal answers to some of your questions. Thomas Elliott wrote: > Hi, > > I'm confused about the nature of the data used in the ALL example in > Bioconductor. The paper (Chiaretti et al 2004) describes a study of > T-cell ALL and doesn't mention BCR-ABL, while the Bioconductor > example (e.g. in the Genome Biology paper) works through a comparison > of BCR/ABL v. ALL1/AF4, which are, I think, markers for B-ALL. I > can't find anything in the phenoData which describes which patients > have T-ALL or B-ALL. > > Thanks. > > Tom Elliott > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hello, the package ALL contains the combined samples from two studies. Patients with T-cell (n=33) and B-cell (n=95) were analyzed separately, and published in those two papers: 4. Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella Vitale, Kathy S. Wang, Franco Mandelli, Robin Foa, Jerome Ritz. Gene Expression Profiles of B-lineage Adult Acute Lymphocytic Leukemia Reveal Distinct Genetic Patterns that Identify Lineage and Distinct Mechanisms of Transformation. Clinical Cancer Research, 2005, 11(20):7209-19. 9. Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella Vitale, Marco Vignetti, Franco Mandelli, Jerome Ritz, Robin Foa. (2004) Gene Expression Profile of Adult T-Cell Acute Lymphocytic Leukemia Identifies Distinct Subsets of Patients with Different Response to Therapy and Survival (Blood, 1 April 2004, Vol. 103, No. 7) Whether it is B- or T-cell leukemia and the stage of the disease is indicated in the phenoData column "BT". > table(ALL$BT) B B1 B2 B3 B4 T T1 T2 T3 T4 5 19 36 23 12 5 1 15 10 2 See the extensive manual page (?ALL) of the data set for a more detailed description. Note that the package ALL only contains the RMA-preprocessed data. There may be a second data package containing the raw CEL files of this data set soon. Regards, Joern Thomas Elliott wrote: > Hi, > > I'm confused about the nature of the data used in the ALL example in > Bioconductor. The paper (Chiaretti et al 2004) describes a study of > T-cell ALL and doesn't mention BCR-ABL, while the Bioconductor > example (e.g. in the Genome Biology paper) works through a comparison > of BCR/ABL v. ALL1/AF4, which are, I think, markers for B-ALL. I > can't find anything in the phenoData which describes which patients > have T-ALL or B-ALL. > > Thanks. > > Tom Elliott > > _______________________________________________ > 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 >

Hello, I did affymetrix gene expression arrays and now I would like to somehow visualize defined spots, e.g. all spots of the probe set 1425088_at. I have a table with the intensities of the individual probes of different probe sets and now I would simply like to compare this values to the pictures of the spots. Does anybody know how I can get these pix? Meike