[BioC] Problem with ArrayQuality Package version 1.12

[Peter White]

Martin - I installed arrayQuality as you show below, but it did not install
automatically with:

source("http://www.bioconductor.org/getBioC.R")
getBioC()

and I am pretty sure it used to. Also, in the R GUI if you select the BioC
repositories, then click Packages...Install Packages... arrayQuality is not
listed on my system?

Thanks,

Peter


-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Friday, July 06, 2007 4:54 PM
To: pwhite at mail.med.upenn.edu
Cc: 'Paquet, Agnes'; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problem with ArrayQuality Package version 1.12

Peter -- something else is up with your system, or did you mean
something else?

> getBioC('arrayQuality')
Running biocinstall version 2.0.8 with R version 2.5.0 
Your version of R requires version 2.0 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.0/bioc/src/contrib/arrayQuality_1.12.0.t
ar.gz'
Content type 'application/x-gzip' length 13832851 bytes
opened URL
==================================================
downloaded 13508Kb

* Installing *source* package 'arrayQuality' ...
...

Martin

"Peter White" <pwhite at mail.med.upenn.edu> writes:

> Hi Agnes,
>
> That solution worked - I actually had to add the following functions to my
> code from version 1.10: gpFlagWt, setCtlCol, qpHexbin, qpImage, and qpS2N.
> Is there anyway to call these functions from the namespace file in the
> current version?
>
> Also, I noticed that arrayQuality is no longer installed with the
getBioC()
> function and it cannot be installed from the "Packages....Install
Packages".
> Is it being removed from the bioconductor package? I hope not as it is
very
> useful and we use it for all our hybs - thanks!
>
> Peter
>
> -----Original Message-----
> From: Paquet, Agnes [mailto:apaquet at medsfgh.ucsf.edu] 
> Sent: Friday, July 06, 2007 3:27 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 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