Question: Problem with ArrayQuality Package version 1.12
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Peter White80
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ADD COMMENTlink modified 12.4 years ago by Paquet, Agnes500 • written 12.4 years ago by Peter White80
Answer: Problem with ArrayQuality Package version 1.12
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gravatar for Paquet, Agnes
12.4 years ago by
Paquet, Agnes500
Paquet, Agnes500 wrote:
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@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
ADD COMMENTlink written 12.4 years ago by Paquet, Agnes500
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@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@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
ADD REPLYlink written 12.4 years ago by Peter White80
Answer: Problem with ArrayQuality Package version 1.12
0
gravatar for Paquet, Agnes
12.4 years ago by
Paquet, Agnes500
Paquet, Agnes500 wrote:
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@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@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@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
ADD COMMENTlink written 12.4 years ago by Paquet, Agnes500
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@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@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@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@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
ADD REPLYlink written 12.4 years ago by Peter White80
Answer: Problem with ArrayQuality Package version 1.12
0
gravatar for Martin Morgan
12.4 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
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]] > > _______________________________________________ > 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
ADD COMMENTlink written 12.4 years ago by Martin Morgan ♦♦ 24k
Answer: Problem with ArrayQuality Package version 1.12
0
gravatar for Martin Morgan
12.4 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
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/arra yQuality_1.12.0.tar.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
ADD COMMENTlink written 12.4 years ago by Martin Morgan ♦♦ 24k
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@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
ADD REPLYlink written 12.4 years ago by Peter White80
Answer: Problem with ArrayQuality Package version 1.12
0
gravatar for Martin Morgan
12.4 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
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
ADD COMMENTlink written 12.4 years ago by Martin Morgan ♦♦ 24k
Answer: Problem with ArrayQuality Package version 1.12
0
gravatar for Paquet, Agnes
12.4 years ago by
Paquet, Agnes500
Paquet, Agnes500 wrote:
Thank you very much for the examples Martin, Agnes -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Fri 7/6/2007 1:37 PM To: Paquet, Agnes Cc: pwhite at mail.med.upenn.edu; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problem with ArrayQuality Package version 1.12 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]] > > _______________________________________________ > 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
ADD COMMENTlink written 12.4 years ago by Paquet, Agnes500
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