Dear madam, sir, I am using Limma with the latest version of bioconductor. After succesfull loading of my Imagene files I want to load a file called SpotTypes.txt as outlined in the Limma usermanual on page 6. Reading the spottypes goes well, but when I apply the spotStatus function I get the following error message: > RG$genes$Status <- spotStatus(spottypes) Error: couldn't find function "spotStatus" If I leave out the spottypes I can create MA plots etc. I'm rather new to R so sometimes I'm puzzled if it is something I do wrong or if something is broken in the package. Could you tell me if this is a bug in Limma or if it is my fault. This is the order of things I do. I attached the SpotTypes.txt file -------------------------------- library(limma) files<-cbind("cy3.tab.txt","cy5.tab.txt") #read the imagene files RG <- read.imagene(files) #set the spottypes spottypes <- readSpotTypes() RG$genes$status <- spotStatus(spottypes) # this goes wrong ------------------------------------ best regards Victor de Jager ---------------------------------- M.Sc. V.C.L. de Jager Erasmus MC, dept of bioinformatics Dr. Molewaterplein 50 3015 GE Rotterdam tel: 31-10-4088454 fax: 31-10-4089468 email: v.dejager@erasmusmc.nl -------------- next part -------------- SpotType ID Name Color Oligo * * black BLANK * ECB_MOUSE_EMPTY_SPOT brown Stratagene - Alien Oligo 1 * ECB_MOUSECTRL_00001_01 red Stratagene - Alien Oligo 2 * ECB_MOUSECTRL_00001_02 red Stratagene - Alien Oligo 3 * ECB_MOUSECTRL_00001_03 red Stratagene - Alien Oligo 4 * ECB_MOUSECTRL_00001_04 red Stratagene - Alien Oligo 5 * ECB_MOUSECTRL_00001_05 red Stratagene - Alien Oligo 6 * ECB_MOUSECTRL_00001_06 red Stratagene - Alien Oligo 7 * ECB_MOUSECTRL_00001_07 red Stratagene - Alien Oligo 8 * ECB_MOUSECTRL_00001_08 red Stratagene - Alien Oligo 9 * ECB_MOUSECTRL_00001_09 red Stratagene - Alien Oligo 10 * ECB_MOUSECTRL_00001_10 red Cot-1 DNA * ECB_MOUSECTRL_00001_11 brown Spot Buffer * ECB_MOUSECTRL_00001_12 brown Poly dA * ECB_MOUSECTRL_00001_13 brown Salmon Sperm DNA * ECB_MOUSECTRL_00001_14 brown M13-Cy3 Oligo Landmark * ECB_MOUSECTRL_00001_15 blue

Victor, > Error: couldn't find function "spotStatus" Actually the function that cannot be found is "spotStatus", not "spotTypes" as indicated by your email subject line. The spotTypes function has been replaced by the controlStatus function. It sounds like you have the Bioconductor 1.3 Release version of the limma user manual. You can upgrade to a more recent version of limma (including recent user manual) from the "development" section of Bioconductor or from: http://bioinf.wehi.edu.au/limma/ > I am using Limma with the latest version of bioconductor. It is helpful to clarify "latest version" with an actual version number. You can look in the DESCRIPTION file of limma or within R, using something like: package.description("limma")["Version"] The latest version of Bioconductor could mean the latest "release" version (quite old) or the latest "development" verison. limma also has its own website: http://bioinf.wehi.edu.au/limma/ which should always have an up-to-date version of limma. You can install from there with install.packages("limma", contriburl="http://bioinf.wehi.edu.au/limma") assuming you have permission to write the first directory in your .libPaths() Regards, James