Hi Christian, Thanks very much for the update on xps. I'll give it a try and let you know how it works. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Wed, 12 Aug 2009, cstrato wrote: > Dear Dick, > > Some weeks ago I have updated package xps to allow some support of the miRNA > aray, and have uploaded "xps_1.5.13" to the BioC development branch. > > Here is the code to create the scheme and import the CEL-files: > > # import scheme: > # note: you need to rename "miRNA-1_0.probe_list.20081203.txt" to > "miRNA-1_0.probe.tab" > libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" > scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir, > paste(libdir,"miRNA-1_0.CDF",sep="/"), > paste(libdir,"miRNA-1_0.probe.tab",sep="/")) > > # import CEL-files (test files from Affymetrix) > datdir <- getwd() > celdir <- "/Volumes/GigaDrive/ChipData/miRNA/genisphere_affymetrix_dataset" > celnames <- c("BrainTotal", "LiverLMW", "LiverTotal") > data.mirna <- > import.data(scheme.mirna,"DatamiRNA",filedir=datdir,celdir=celdir,ce lnames=celnames) > > As you see, you need to rename the probe file and you cannot use the special > Affymetrix annotation file since it does not follow the standard annotation > layout. > > > In a new R session you can load the scheme and data files as usual, and do RMA: > > # load scheme and data > scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" > datdir <- getwd() > scheme.mirna <- root.scheme(paste(scmdir,"Scheme_miRNA_1_0.root",sep="/")) > data.mirna <- root.data(scheme.mirna, > paste(datdir,"DatamiRNA_cel.root",sep="/")) > > # RMA > data.rma <- > rma(data.mirna,"miRNA_RMA",tmpdir="",background="pmonly",normalize=T) > > # get expression level data.frames > expr.rma <- validData(data.rma) > head(expr.rma) > > > You can also do some visualization: > > # for raw data you need to attach data first > data.mirna <- attachMask(data.mirna) > data.mirna <- attachInten(data.mirna) > > # plots > image(data.mirna) > hist(data.mirna) > boxplot(data.mirna) > hist(data.rma) > boxplot(data.rma) > > Please note that currently all probesets for all different organisms are used > for RMA. > > Since I have no access to miRNA data, I would be interested in reports from > users trying xps for miRNA, especially if RMA normalization gives reasonable > results. > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > > Dick Beyer wrote: >> Are there any plans to support the new affy microRNA chip: miRNA- 1_0? >> >> Thanks, >> Dick >> >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ >> 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 >> >> > >