Dear List I wonder if any of you may have used package "FLUSH.LVS.bundle" with Affymetrix Gene 1.0 ST arrays. I get an error when processing the RA object. I supose this error is related because initially was designed to use with arrays with mm probes, but in principle you can use without it, for the moment I cannot handle to solve it, but I think the solution may be possible. Here is the code and the error I get. Thank you very much. library("affy") library("FLUSH.LVS.bundle") data <- ReadAffy() RA.fit <- compute.RA(data) Fitting models | | |#Error in t(contr.helmert(nprobes)) : error in evaluating the argument 'x' in selecting a method for function 't' traceback() 6: t(contr.helmert(nprobes)) 5: as.vector(data) 4: matrix(rep(t(contr.helmert(nprobes)), nsamples), byrow = T, ncol = nprobes - 1) 3: make.design(nsamples = nsamples, nprobes = tabProbes[i]) 2: compute.RA(data) 1: compute.RA(data) sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=ca_ES.utf8 LC_NUMERIC=C [3] LC_TIME=ca_ES.utf8 LC_COLLATE=ca_ES.utf8 [5] LC_MONETARY=C LC_MESSAGES=ca_ES.utf8 [7] LC_PAPER=ca_ES.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=ca_ES.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hugene10stv1cdf_2.7.1 FLUSH.LVS.bundle_1.3.1 affyPLM_1.26.0 [4] preprocessCore_1.12.0 gcrma_2.22.0 quantreg_4.53 [7] SparseM_0.86 affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 AnnotationDbi_1.12.0 Biostrings_2.18.2 [4] DBI_0.2-5 IRanges_1.8.4 RSQLite_0.9-4 [7] splines_2.12.0 tools_2.12.0 Oriol Senan Campos Non Linear Dynamics Non Linear Optics Group Universitat Politècnica de Catalunya, Campus de Terrasa * +34 93 739 *8835 [[alternative HTML version deleted]]

On 12/15/2010 07:35 AM, Oriol SENAN wrote: > Dear List > > I wonder if any of you may have used package "FLUSH.LVS.bundle" with > Affymetrix Gene 1.0 ST arrays. I get an error when processing the RA object. > I supose this error is related because initially was designed to use with > arrays with mm probes, but in principle you can use without it, for the > moment I cannot handle to solve it, but I think the solution may be > possible. Here is the code and the error I get. > > Thank you very much. > > library("affy") > library("FLUSH.LVS.bundle") Hi Oriol -- FLUSH.LVS.bundle is not a Bioconductor package; you're likely to get better help by communicating with the package maintainer directly. packageDescription('FLUSH.LVS.bundle')$Maintainer Martin > data <- ReadAffy() > RA.fit <- compute.RA(data) > > Fitting models > | | > |#Error in t(contr.helmert(nprobes)) : > error in evaluating the argument 'x' in selecting a method for function > 't' > > traceback() > 6: t(contr.helmert(nprobes)) > 5: as.vector(data) > 4: matrix(rep(t(contr.helmert(nprobes)), nsamples), byrow = T, ncol = > nprobes - > 1) > 3: make.design(nsamples = nsamples, nprobes = tabProbes[i]) > 2: compute.RA(data) > 1: compute.RA(data) > > sessionInfo() > > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=ca_ES.utf8 LC_NUMERIC=C > [3] LC_TIME=ca_ES.utf8 LC_COLLATE=ca_ES.utf8 > [5] LC_MONETARY=C LC_MESSAGES=ca_ES.utf8 > [7] LC_PAPER=ca_ES.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=ca_ES.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hugene10stv1cdf_2.7.1 FLUSH.LVS.bundle_1.3.1 affyPLM_1.26.0 > [4] preprocessCore_1.12.0 gcrma_2.22.0 quantreg_4.53 > [7] SparseM_0.86 affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 AnnotationDbi_1.12.0 Biostrings_2.18.2 > [4] DBI_0.2-5 IRanges_1.8.4 RSQLite_0.9-4 > [7] splines_2.12.0 tools_2.12.0 > > Oriol Senan Campos > Non Linear Dynamics Non Linear Optics Group > Universitat Polit?cnica de Catalunya, Campus de Terrasa > * +34 93 739 *8835 > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793