Dear List Members, I am getting the following error when I run maQualityPlot(RGlist) in arrayQuality package. Error in seq.default(0, 1, length = min(17, maxcnt)) : length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf I have all updated packages installed from the Bioconductor. How can I resolve this? Thanks. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

On 30 Sep 2005, khan at cshl.edu wrote: > I have all updated packages installed from the Bioconductor. > How can I resolve this? Please include sessionInfo() output, this is a much more reliable way of telling us what versions you are using. > Dear List Members, > I am getting the following error when I run maQualityPlot(RGlist) in > arrayQuality package. > > Error in seq.default(0, 1, length = min(17, maxcnt)) : > length must be non-negative number > In addition: Warning message: > no finite arguments to max; returning -Inf The output of traceback() right after you get the error message might also be helpful. + seth

Hi, This error occurs when spot types (e.g. positive controls, negative controls...) are not set up properly in the RGlist or marrayRaw object and/or the spot type's look-up table named controlCode is not matching the various spot types on the array. The spot types used in arrayQuality are defined in a 2 column matrix called controlCode. By default, it is set to the various types of controls we use in the Genomics Core at UCSF. You can see the default values in controlCode by typing in R: > controlCode Pattern Name 1 "Buffer" "Buffer" 2 "Empty" "Empty" 3 "EMPTY" "Empty" 4 "AT" "Negative" 5 "NC" "Negative" 6 - To define spot types in your RGlist object: The easiest way to do it is to create a tab-delimited text file named SpotTypes.txt. You can find more explanations about SpotType files and how to set up your controls in your RGlist object in the limma User's Guide. - To define your own spot type's look-up table: You will need to replace the default values in controlCode with your values. You should be able to use the same SpotType file for this step. You can read it into arrayQuality using the function readcontrolCode. It is also possible to create a new controlCode matrix directly. More details for this step are provided in the last section of arrayQuality user's guide. controlCode <- readcontrolCode(file="mySpotTypes.txt", controlId="ID") Please let me know if you have any more problems. Best, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Khan, Sohail Sent: Friday, September 30, 2005 9:14 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Error:"arrayQuality" Dear Members, In regards to my previous question here is my session out. R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > library(arrayQuality) Loading required package: marray Loading required package: limma Loading required package: convert Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] "arrayQuality" [1] "Checking for missing packages" Garbage collection 60 = 53+4+3 (level 2) ... 102028 cons cells free (21%) 5.0 Mbytes of heap free (84%) [1] "Loading required packages" Attaching package: 'mclust' The following object(s) are masked from package:stats : density Warning message: package 'marray' was built under R version 2.2.0 > files<-c("43.gpr","48.gpr","93.gpr","95.gpr") > files [1] "43.gpr" "48.gpr" "93.gpr" "95.gpr" > RG<-read.maimages(files,source="genepix") Read 43.gpr Read 48.gpr Read 93.gpr Read 95.gpr > results<-maQualityPlots(RG) Loading required package: hexbin Loading required package: grid Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Error in if is.int(totalPlate)) { : argument is of length zero Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Dear Members, In regards to my previous question here is my session out. R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > library(arrayQuality) Loading required package: marray Loading required package: limma Loading required package: convert Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] "arrayQuality" [1] "Checking for missing packages" Garbage collection 60 = 53+4+3 (level 2) ... 102028 cons cells free (21%) 5.0 Mbytes of heap free (84%) [1] "Loading required packages" Attaching package: 'mclust' The following object(s) are masked from package:stats : density Warning message: package 'marray' was built under R version 2.2.0 > files<-c("43.gpr","48.gpr","93.gpr","95.gpr") > files [1] "43.gpr" "48.gpr" "93.gpr" "95.gpr" > RG<-read.maimages(files,source="genepix") Read 43.gpr Read 48.gpr Read 93.gpr Read 95.gpr > results<-maQualityPlots(RG) Loading required package: hexbin Loading required package: grid Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Error in if is.int(totalPlate)) { : argument is of length zero Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076