[BioC] Problem with ArrayQuality Package version 1.12

[Martin Morgan]

Hi Peter & Agnes -- variables inside namespaces can be accessed with

arrayQuality:::gpFlagWt(mraw at maW)

or

do.call("gpFlagWt", list(mraw at maW), envir=getNamespace("arrayQuality"))

It's probably appropriate not to export these variables from the
name space, since they are really implementation details that the user
can't realy rely on to stay constant.

Martin

"Paquet, Agnes" <apaquet at medsfgh.ucsf.edu> writes:

> Hi Peter,
>  
> I just remembered now that we have added a namespace file for
> arrayQuality in the new release, and the function you are trying to
> use is not exported anymore. I need to do some check to see if
> exporting these function would conflit with anything else before I can
> change the file, so the easiest fix for now would be to add your own
> flagging and coloring functions in your code.
>  
> Regards,
>  
> Agnes
>  
>  
>
> ________________________________
>
> From: Peter White [mailto:pwhite at mail.med.upenn.edu] Sent: Fri
> 7/6/2007 11:56 AM To: Paquet, Agnes; bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] Problem with ArrayQuality Package version 1.12
>
>
>
> Dear Agnes,
>
> I was using your maQualityPlots code in my own function (see part of
> it below). The problem seems to be that in the newer version if I load
> the arrayQuality library I get an object not found error if I type
> gpFlagWt or setCtlCol. When I install the old version and type them in
> it returns the function?
>
> Could it be a difference in how it was compiled in R 2.5.1? I can run
> the maQualityPlots(mrawObj) function just fine with the new version,
> just not as laid out below.
>
> Thanks,
>
> Peter
>
>
> fgcQualityPlots <- function (mrawObj, mnormObj = NULL, postProcessed =
> FALSE, headerInfo = "", save = TRUE, dev = "png",
>     col = NULL, badspotfunction = NULL, controlId = c("ID", "Name"),
>     DEBUG = FALSE, ...)  { require(arrayQuality, quietly=TRUE,
> warn.conflicts=TRUE, keep.source=getOption("keep.source.pkgs"));
> require(marray, quietly=TRUE, warn.conflicts=TRUE,
> keep.source=getOption("keep.source.pkgs")); if (!exists("workingDir"))
> {workingDir = winDialogString("Please enter the working directory:",
> "D:\\Array_Experiments")} if (!exists("prefixName")) {workingDir =
> winDialogString("Please enter a Prefix Name for the experiment:",
> "Experiment")} if (!exists("analysisLog")) analysisLog = FALSE;
>
>     require(hexbin)
>     if (DEBUG)
>         print("function starting")
>     controlId <- controlId[1]
>     if (setequal(class(mrawObj), "RGList")) { #If your data is a
> RGList this function will convert it to an marray object
>         mrawTmp <- as(mrawObj, "marrayRaw")
>         mrawObj <- mrawTmp
>         rm(mrawTmp)
>     }
>     if (DEBUG)
>         print(dim(mrawObj))
>     for (i in 1:dim(mrawObj)[2]) {
>         mraw <- mrawObj[, i]
>         if(!is.null(mnormObj) & postProcessed==TRUE) {
>             mnormObjTmp <- mnormObj[, i]
>         }
>         opt <- list(...)
>
> #Function to re-evaluate weights based upon flags
>
>         if (DEBUG)
>             print("Re-evaluate Weight")
>         if (missing(badspotfunction) || is.null(badspotfunction)) {
>             tmp <- do.call("gpFlagWt", list(mraw at maW))
>             mraw at maW <- tmp
>         }
>         else if (!is.null(badspotfunction))
>             mraw at maW <- do.call(badspotfunction, list(mraw at maW))
>        
>         ifelse(missing(col), colcode <- setCtlCol(mraw), colcode <-
> col)
>         if (DEBUG)
>             cat("check Control color code", colcode, "\n")
>
> -----Original Message----- From: Paquet, Agnes
> [mailto:apaquet at medsfgh.ucsf.edu] Sent: Friday, July 06, 2007 2:05 PM
> To: pwhite at mail.med.upenn.edu; bioconductor at stat.math.ethz.ch Subject:
> RE: [BioC] Problem with ArrayQuality Package version 1.12
>
> Hi Peter,
>
> I just tried to run the function meeboQuality, which calls gpFlagWt, with
> the same R and BioC setting as you and it worked fine. Could you please
> email me the R code you are trying to run so that I can reproduce the error?
>
>
> Thank you very much,
>
> Agnes
> ________________________________
>
> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Peter White
> Sent: Fri 7/6/2007 8:57 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Problem with ArrayQuality Package version 1.12
>
>
>
> I am running R 2.51 and Bioconductor 2.0. When I attempt to use the
> arrayQuality package I get the message:
>
>
>
> Error in do.call("gpFlagWt", list(mraw at maW)) :
>
>         could not find function "gpFlagWt"
>
>
>
> I installed a previous version of the package, 1.10, and it works fine as
> the missing function is included with that download. Could you please update
> the package or give me a solution to the problem.
>
>
>
> Thanks,
>
>
>
> Peter
>
>
>
> Peter White, Ph.D.
> Functional Genomics Core
> Department of Genetics
> University of Pennsylvania
> Philadelphia, PA 19104-6145
>
>
>
>
>         [[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org