Your original code had CV.rep.probes(aa,"zebrafish.db0 ",... I'm assuming this was just a typo in recopying the code, as it wouldn't work if you had the space after the 0. By sessionInfo(), I meant the output of the sessionInfo() function. What you just posted is different than before. You have an error loading beadarray and you haven't loaded zebrafish.db0, leading to a different error than originally. Please try to be consistent, otherwise it's very difficult to pinpoint the problem. As it is, I believe the issue is that Agi4x44PreProcess::CV.rep.probes always expects a ACCNUM mapping and none exist in zebrafish.db0. The solution here would be to get them to talk to one another properly. Marc, is there be a recommended way to deal with this? Is there a basic mapping that every annotation package should use? Or should a package maintainer be aware of all existing variations that exist? Francois On 11/12/2009 10:35 PM, Neel Aluru wrote: > Thanks, Francois. I am a beginner to R and slowly trying to learn. I appreciate your comments. Now I have pasted the session info. You may be right with regard to ACCNUM mapping. I looked in the zebrafish.db0 package and cannot find the ACCNUMmapping. I do not understand what you meant by space in "zebrafish.db0". > > Thanks once again, > > Sincerely, Neel > > Following is the session info. > R version 2.9.2 (2009-08-24) > Copyright (C) 2009 The R Foundation for Statistical Computing >> getwd() > [1] "/Users/Neel" >> setwd("/Users/Neel/agilent") >> getwd() > [1] "/Users/Neel/agilent" > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > Loading required package: limma > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: genefilter > Loading required package: affyPLM > Loading required package: affy > > Attaching package: 'affy' > The following object(s) are masked from package:Agi4x44PreProcess : > plotDensity > Loading required package: gcrma > Loading required package: Biostrings > Loading required package: IRanges > Attaching package: 'IRanges' > The following object(s) are masked from package:base : > > cbind, > duplicated, > order, > pmax, > pmax.int, > pmin, > pmin.int, > rank, > rbind, > rep.int, > sapply, > sort, > table, > unique > > Loading required package: preprocessCore > Attaching package: 'affyPLM' > The following object(s) are masked from package:Agi4x44PreProcess : > RLE > The following object(s) are masked from package:stats : > resid, > residuals, > weights > Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : > there is no package called 'beadarray' > Error: package/namespace load failed for 'arrayQualityMetrics' > Loading required package: tcltk > Loading Tcl/Tk interface ... done > > limmaGUI can be launched by typing limmaGUI() > > Attaching package: 'limmaGUI' > The following object(s) are masked from package:limma : > limmaUsersGuide > limmaGUI can be launched by typing limmaGUI() > Attaching package: 'limmaGUI' > The following object(s) are masked from package:limma : > limmaUsersGuide >> library("Agi4x44PreProcess") >> targets=read.targets(infile="infile.txt") > Target File > X FileName Treatment GErep > conta cont1 conta.txt control 1 > contb cont2 contb.txt control 2 > contc cont3 contc.txt control 3 > contd cont4 contd.txt control 4 > pcba pcb1 pcba.txt pcb 1 > pcbb pcb2 pcbb.txt pcb 2 > pcbc pcb3 pcbc.txt pcb 3 > pcbd pcb4 pcbd.txt pcb 4 > > > aa=read.AgilentFE(targets, makePLOT=TRUE) > Read conta.txt > Read contb.txt > Read contc.txt > Read contd.txt > Read pcba.txt > Read pcbb.txt > Read pcbc.txt > Read pcbd.txt > > RGList: > dd$R: 'gProcessedSignal' > dd$G: 'gMeanSignal' > dd$Rb: 'gBGMedianSignal' > dd$Gb: 'gBGUsed' > >> CV.rep.probes(aa, "zebrafish.db", foreground="MeanSignal", raw.data= TRUE, writeR=FALSE,targets) > > ------------------------------------------------------ > Non-CTRL Replicated probes > foreground: MeanSignal > FILTERING BY ControlType FLAG > RAW DATA: PROBES AFTER ControlType FILTERING: 42990 > > Error: getAnnMap: zebrafish.db package not attached and load is FALSE > Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) : > error in evaluating the argument 'envir' in selecting a method for function 'mget' > >> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = TRUE, makePLOTpost = TRUE) > BACKGROUND CORRECTION AND NORMALIZATION > > foreground: MeanSignal > background: BGMedianSignal > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > > BGmethod: half > NORMmethod: quantile > OUTPUT in log-2 scale > > ------------------------------------------------------ > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > Hit<return> to see next plot: > End of the session > > > On Nov 12, 2009, at 9:36 PM, Francois Pepin wrote: > >> Hi Neel, >> >> in cases like this, supplying the sessionInfo() is a good idea, as it lets everyone know which versions you are using. As per the posting guide (see the URL at the bottom of this e-mail), having the code snippet initially would also have been helpful. >> >> I don't have the zebrafish.db0 package installed, so I can't say for sure what the issue is. I don't think you should have the space in "zebrafish.db0 ". It might also be that the zebrafish.db0 package does not have the ACCNUM mapping. >> >> Now that we've got more information, the others can chime in with more insight. >> >> Francois >> >> On 11/12/2009 09:08 PM, Neel Aluru wrote: >>> Hi Francois, >>> >>> Thanks for your reply. I am trying to calculate the replicated probe coefficient of variation and having trouble understanding it. Here is the syntax I am writing for it. >>> >>>> CV.rep.probes(aa,"zebrafish.db0 ",foreground ="MeanSignal", raw.data=TRUE, writeR = TRUE, targets) >>> The error message is >>> >>> Non-CTRL Replicated probes >>> foreground: MeanSignal >>> FILTERING BY ControlType FLAG >>> RAW DATA: PROBES AFTER ControlType FILTERING: 42990 >>> >>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) : >>> object 'zebrafish.db0ACCNUM' not found >>> Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) : >>> error in evaluating the argument 'envir' in selecting a method for function 'mget' >>> >>> I defined "aa" for reading agilent FE files. >>> >>> I am not sure if I am doing something wrong. I really appreciate any suggestions how to proceed with it. >>> >>> Thanks, >>> >>> Sincerely, Neel >>> >>> On Nov 12, 2009, at 3:31 PM, Francois Pepin wrote: >>> >>>> Hi Neel. >>>> >>>> I'm not sure which database you are talking about here. >>>> >>>> I haven't used zebrafish arrays, but my experience with human and mouse is that there is very little variation between duplicated probes (ie same sequence and probe id). I would be surprised if zebrafish is any different, as those differences would be purely technical and only depend on the protocol, the reagents used and the person performing the manipulations. >>>> >>>> Maybe you could clarify if I'm not reading this properly, as I'm confused what a database would have to do with this. >>>> >>>> Francois >>>> >>>> On 11/12/2009 03:19 PM, Neel Aluru wrote: >>>>> Hello, >>>>> >>>>> Does any one has Agilent zebrafish 4x44 database to use for calculating % CV of replicated probes. >>>>> >>>>> Thank you, >>>>> >>>>> Neel >>>>> >>>>> >>>>> Neel Aluru >>>>> Postdoctoral Scholar >>>>> Biology Department >>>>> Woods Hole Oceanographic Institution >>>>> Woods Hole, MA 02543 >>>>> USA >>>>> 508-289-3607 >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> Neel Aluru >>> Postdoctoral Scholar >>> Biology Department >>> Woods Hole Oceanographic Institution >>> Woods Hole, MA 02543 >>> USA >>> 508-289-3607 >>> >>> >>> >> > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > >