James, I see. Thank you very much! Best regards Galina -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, September 27, 2010 3:56 PM To: Glazko, Galina Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] PM values for probes in a probeset: background corrected and normalized, but not summarized? Hi Galina, On 9/27/2010 3:24 PM, Glazko, Galina wrote: > Dear list, > > I am wondering, is it possible to get Affy PM values for probes in a probeset, > which will be background corrected and normalized, but not summarized? > > I know that I can get just intensities of probes, but do not know whether it is possible to > do for them all steps - backgound correction and normalization, but without summarization. > > I would appreciate if someone could clarify this for me! An example: > library(affydata) > data(Dilution) > abatch <- bg.correct(Dilution, "rma") > abatch <- normalize(abatch, "quantiles") > pm(abatch, "1007_s_at") 20A 20B 10A 10B 1007_s_at1 158.82305 160.04805 184.92305 199.94805 1007_s_at2 479.42305 399.03555 370.37305 382.37305 1007_s_at3 670.62305 570.12305 625.69805 571.37305 1007_s_at4 1619.72305 1764.99805 1566.96055 1564.28555 1007_s_at5 2264.32305 1931.99805 2094.32305 1845.04805 1007_s_at6 1313.32305 1295.56055 1258.89805 1142.59805 1007_s_at7 334.57305 278.37305 293.79805 301.54805 1007_s_at8 285.17305 285.77305 322.57305 282.87305 1007_s_at9 173.07305 150.98555 188.07305 157.44805 1007_s_at10 534.62305 638.42305 587.42305 538.02305 1007_s_at11 510.99805 471.69805 450.42305 473.49805 1007_s_at12 304.42305 264.67305 222.37305 267.27305 1007_s_at13 292.27305 264.67305 229.87305 261.94805 1007_s_at14 21.67983 18.39805 17.99024 13.83471 1007_s_at15 77.57305 82.24805 122.37305 97.42305 1007_s_at16 358.57305 368.24805 269.74805 302.42305 > pm(Dilution, "1007_s_at") 20A 20B 10A 10B 1007_s_at1 338.8 232.0 290.0 188.3 1007_s_at2 790.0 455.0 481.3 304.0 1007_s_at3 1059.0 611.0 748.3 423.5 1007_s_at4 2373.0 1679.0 1756.0 1061.5 1007_s_at5 3239.3 1821.0 2346.3 1249.0 1007_s_at6 1957.5 1268.0 1418.0 780.3 1007_s_at7 584.8 342.0 403.0 252.5 1007_s_at8 516.0 348.5 432.8 240.5 1007_s_at9 359.0 223.3 293.3 161.3 1007_s_at10 869.0 673.0 707.0 401.5 1007_s_at11 835.0 521.8 563.0 361.5 1007_s_at12 543.0 329.0 329.0 231.0 1007_s_at13 526.0 329.0 336.8 227.3 1007_s_at14 146.0 96.0 114.8 71.3 1007_s_at15 225.3 158.8 224.3 124.0 1007_s_at16 618.0 426.0 377.8 253.0 Best, Jim > > thank you! > Best regards > Galina > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues