Dear List, I have a problem. I want to get the information about the Hgu133_Plus2 as follow, My interest is which probes are included in each probesets? where is the location of these probes (x, y) in the microarray? I know all the information are in Hgu133_Plus2 cdf file. My problem is how I can extract these information out of this cdf file in R? First step, like making a table: probests1 probe1 x1 y1 probe2 x2 y2 probe3 x3 y3 probe4 x4 y4 ... ... probests2 probe1 x1 y1 probe2 x2 y2 probe3 x3 y3 probe4 x4 y4 ... ... probests54675 probe1 x1 y1 probe2 x2 y2 probe3 x3 y3 probe4 x4 y4 in further step, how I can extract the intensity for each probe in .cel file of each sample? probests1 probe1 x1 y1 intensity1 probe2 x2 y2 intensity2 probe3 x3 y3 intensity3 probe4 x4 y4 intensity4 ... ... If anyone know how I can do program in R and get this table for each sample (array)? Many thanks in advance. Bests, Meiyin [[alternative HTML version deleted]]

Hi Meiyin, meiyin gao wrote: > Dear List, > > I have a problem. > > I want to get the information about the Hgu133_Plus2 as follow, > > My interest is which probes are included in each probesets? where is the > location of these probes (x, y) in the microarray? > > I know all the information are in Hgu133_Plus2 cdf file. > > My problem is how I can extract these information out of this cdf file in R? > > First step, like making a table: > > probests1 probe1 x1 y1 > probe2 x2 y2 > probe3 x3 y3 > probe4 x4 y4 > ... > ... > probests2 probe1 x1 y1 > probe2 x2 y2 > probe3 x3 y3 > probe4 x4 y4 > ... > ... > probests54675 probe1 x1 y1 > probe2 x2 y2 > probe3 x3 y3 > probe4 x4 y4 How about a list instead? > index.list <- head(as.list(hgu133plus2cdf)) > xy.list <- lapply(index.list, function(x) indices2xy(x[,1], cdf="hgu133plus2cdf")) $`243726_at` x y [1,] 852 919 [2,] 895 1067 [3,] 576 343 [4,] 221 497 [5,] 1101 125 [6,] 415 915 [7,] 981 845 [8,] 539 239 [9,] 755 565 [10,] 366 187 [11,] 958 27 $`1555812_a_at` x y [1,] 702 403 [2,] 245 159 [3,] 817 157 [4,] 245 801 [5,] 1065 339 [6,] 668 897 [7,] 1116 87 [8,] 360 949 [9,] 669 69 [10,] 92 649 [11,] 265 617 $`215958_at` x y [1,] 280 735 [2,] 89 273 [3,] 45 1065 [4,] 1024 1111 [5,] 315 1131 [6,] 563 447 [7,] 653 517 [8,] 20 547 [9,] 520 13 [10,] 624 93 [11,] 985 311 > > in further step, how I can extract the intensity for each probe in .cel file > of each sample? > probests1 probe1 x1 y1 intensity1 > probe2 x2 y2 intensity2 > probe3 x3 y3 intensity3 > probe4 x4 y4 intensity4 Two steps: We need an AffyBatch first dat <- ReadAffy() int.data <- pm(dat, LISTRUE = TRUE, names(xy.list)) final.table <- mapply(cbind, xy.list, int.data, SIMPLIFY = FALSE) Best, Jim > ... > ... > > If anyone know how I can do program in R and get this table for each sample > (array)? > > Many thanks in advance. > > Bests, > > Meiyin > > [[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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623