[BioC] Problem with ArrayQuality Package version 1.12

[Paquet, Agnes]

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




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