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