Dear Sir or Madam, I would like to analyse the copy number variation data from Affymetrix Mouse Diversity Array. I have not found any information on your website about this particular array. I have tried to build the annotation files which are required by aroma but without success. I have few questions regarding that: 1: Is aroma.affymetrix able to analyse the "Mouse Diversity Array" ? 2: I tried to build the "UGP" file directly from NetAffx annotation files using the code on your website, however I am getting the following error. ## library("aroma.affymetrix") ## ## create UGP from NetAffx files cdf <- AffymetrixCdfFile$byChipType("MOUSEDIVm520650") ## ## Creates an empty UGP file for the CDF, if missing. ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=c("na30", "RI20100526")) ## ## Import NetAffx unit position data csv <- AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", otags=".na30") Error in list(`AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", tags = ".na30")` = <environment>, : [2010-05-26 15:11:00] Exception: File format error of the tabular file ('annotationData/chipTypes/MOUSEDIVm520650/NetAffx/MOUSEDIVm520650.na3 0.annot.csv'): \ line 1 did not have 12 elements at throw(Exception(...)) at throw.default("File format error of the tabular file ('", getPathname(this), "'): ", ex$message) at throw("File format error of the tabular file ('", getPathname(this), "'): ", ex$message) at value[[3]](cond) at tryCatchOne(expr, names, parentenv, handlers[[1]]) at tryCatchList(expr, classes, parentenv, handlers) at tryCatch({ at verify.TabularTextFile(this, ...) at verify(this, ...) at this(...) at newInstance.Class(clazz, ...) at newInstance(clazz, ...) at newInstance.Object(static, pathname) at newInstance(static, pathname) at method(static, ...) at AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", tags = ".na30") In addition: Warning message: In read.table(3L, header = TRUE, colClasses = c(NA_character_, NA_character_, : not all columns named in 'colClasses' exist 3. I tried it also by using the "manual" approach using the tab=delimited file, however it seems to me that the mitochondria probes are skipped (NA values in ugp[,1] but valid values in ugp[,2]). Another problem is that some positions for other chromosomes are not loaded in properly (valid values in ugp[,1] but NA values in ugp[,2]). Here is the sessionInfo: R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_1.6.0 aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.6.0 aroma.light_1.16.0 [7] matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.1 digest_0.4.2 R.utils_1.4.0 [13] R.oo_1.7.2 R.methodsS3_1.2.0 RColorBrewer_1.0-2 loaded via a namespace (and not attached): [1] tools_2.11.0 Best Regards Robert -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100