[BioC] Problem with ArrayQuality Package version 1.12

[Martin Morgan]

Hi Peter --

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

> Martin - I installed arrayQuality as you show below, but it did not install
> automatically with:
>
> source("http://www.bioconductor.org/getBioC.R")
> getBioC()

Taking a peak at archived versions, I suspect that arrayQuality has
not been in the default package list...

> 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?

... and I think this is a problem at our (for your version of R, I bet
no Bioconductor packages are showing up!); we'll investigate.

Martin

> 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
>

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org