Hi, I am trying to run oneChannelGUI, analysing data based on the Affy Gene 1.0 ST Array. I installed the library from http://www.bioinformatica.unito.it/downlo ads/hugene10stv1cdf_1.0.0.tar.gz (I am not sure how legitimate this is :-) ). When running the 'Table of genes ranked in order of differential expression' option in oneChannelGUI it generated several errors (in the tcl/tk interface,see below) and wouldn't generate the top table of results. It looks like it is trying to load 'hugene10stv1' rather than 'hugene10stv1cdf'. If this is the problem, is there a workaround or an official hugene10stv1 library that works with this package? Errors in R Shell ================= > ls() [1] "affylmGUIenvironment" "ReturnVal" Warning messages: 1: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former 2: In file(con, "w") : file("") only supports open = "w+" and open = "w+b": using the former 3: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value 4: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value 5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'hugene10stv1' > library("hugene10stv1") Error in library("hugene10stv1") : there is no package called 'hugene10stv1' Errors in Tcl/Tk OneChannelGUI ============================== Error in stop("need data package: ", annlib) : object "annlib" not found Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1ENTREZID" of mode "environment" was not found Error in get(paste(lib, name, sep = ""), mode = "environment"): variable "hugene10stv1SYMBOL" of mode "environment" was not found Error in dim(data) <- dim : attempt to set an attribute on NULL Error in names(x)<-value : 'names' attribute[3] must be same length as the vector[1] ========================== > sessionInfo() R version 2.6.1 (2007-11-26) sparc-sun-solaris2.9 locale: /en_GB/C/en_GB/en_GB/en_GB/en_GB attached base packages: [1] tcltk tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hugene10stv1cdf_1.0.0 oneChannelGUI_1.4.2 tkWidgets_1.16.0 [4] DynDoc_1.16.0 widgetTools_1.14.0 affylmGUI_1.12.0 [7] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 [10] limma_2.12.0 Biobase_1.16.2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 Thanks for any help, Steve ========================================== Medical Sciences Division Weatherall Institute of Molecular Medicine Oxford University

Dear Steve I suggest you to download the latest version of oneChannelGUI 1.6.2 Due to various problems with cdfs I moved, in the latest version of oneChannelGUI, to the use of APT tools for the calculation of probe set summaries also for gene arrays. You have to install by yourself APT tools on your computer. Than using the function "oneChannelGUI: Set Affymetrix apt tools folder" located in the general menu you will set the apt tool parameter in oneChannelGUI. Subsequently with the function "oneChannelGUI: Set library folder and install Affy gene/Exon library files" you will install in the oneChannelGUI dir all the Affymetrix library files needed to analyze gene and exon arrays. There is in "file" menu a specific radio button for GENE arrays. Ones summaries are calculated those are stored in an ExpressionSet object and you can analyze them using any of the statistical tools interfaced in oneChannelGUI. Let me know if you get any further problem in running the gene array analysis Cheers Raffaele >##################### >Hi, >I am trying to run oneChannelGUI, analysing data based on the Affy Gene 1.0 ST Array. >I installed the library from http://www.bioinformatica.unito.it/downl oads/hugene10stv1cdf_1.0.0.tar.gz (I >am not sure how legitimate this is :-) ). >When running the 'Table of genes ranked in order of differential expression' option in oneChannelGUI it >generated several errors (in the tcl/tk interface,see below) and wouldn't generate the top table >of results. It looks like it is trying to load 'hugene10stv1' rather than 'hugene10stv1cdf'. If this is >the problem, is there a workaround or an official hugene10stv1 library that works with this package? ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: www.bioinformatica.unito.it