Dear Henrik Bengtsson, we would like to use the CRMA v2 for our work. Unfortunately we receive errors.
First we use a Linux system (Suse 11.2). I installed R (version 2.11.0) without any problems. Afterwards I followed your instructions on your webpage (http://aroma- project.org/install) to install CRMA v2. After the installation process I received this warning: "In packageDescription(pkg) : no package 'DNAcopy' was found" Nevertheless the program works fine at the beginning. I followed your instructions on this page: http://aroma-project.org/vignettes/CRMAv2 The analysis startup and the declaration of the raw data set work without errors. The section "Step 1 - Calibration for crosstalk between allele probe pairs" also works as long as I come to the command: > array <- 1xlim <- c(-500,15000) Fehler: Unerwartetes Symbol in "array <- 1xlim" > plotAllelePairs(acc, array=array, pairs=1:6, what="input", xlim=xlim/3) Fehler in list(`plotAllelePairs(acc, array = array, pairs = 1:6, what = "input", xlim = xli` = <environment>, : [2010-05-11 10:40:58] Exception: Argument 'array' is not a vector: function at throw(Exception(...)) at throw.default(sprintf("Argument '%s' is not a vector: %s", .name, storage.m at throw(sprintf("Argument '%s' is not a vector: %s", .name, storage.mode(x))) at getVector.Arguments(static, x, ..., .name = .name) at getVector(static, x, ..., .name = .name) at getNumerics.Arguments(static, ..., asMode = "integer", disallow = disallow) at getNumerics(static, ..., asMode = "integer", disallow = disallow) at getIntegers.Arguments(static, x, ..., range = range, .name = .name) at getIntegers(static, x, ..., range = range, .name = .name) at getIndices.Arguments(static, ..., length = length) at getIndices(static, ..., length = length) at method(static, ...) at Arguments$getIndex(array, range = c(1, Inf)) at plotAllelePairs.AllelicCrosstalkCalibration(acc, array = array, pairs = 1:6 at plotAllelePairs(acc, array = array, pairs = 1:6, what = "input", xlim ...... First I receive the error: unexpected symbol in "array <- 1xlim" Do you have experience with this error? I don't know whether the following error "Argument 'array' is not a vector" occurs as a consequence of the first error. I removed the "^M" symbols in the CEL files. But this error occurs with "^M" and without it. Do you know an accurate dataset, which we can use as basis to test the software with a unix system. I hope you find some time to answer my request. Thanks in advance. Cheers Markus -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
