I thought I fixed this in aroma.core 2.9.2, but I guess it wasn't enough.
For now try to load the R.cache package on startup - that should work
around the problem. Let me know if it works.
Henrik
On Jun 20, 2013 5:46 PM, "rangerq" <ranger...@gmail.com> wrote:
> Hi,
>
> I got an error when I processed a Affy Human Gene 1.0 ST array data with
> 33 samples.
>
> The error message is
>
> Error in UseMethod("getChecksum") :
> no applicable method for 'getChecksum' applied to an object of class
> "list"
>
> I got this error in performing quantile normalization. R is updated to the
> latest R3.0.1 and I used aroma.affymetrix_2.9.4 and aroma.core_2.9.5.
>
> Please help to solve this problem.
>
> Thanks,
> Qihao Qi
> BRB-ArrayTools Development Team
>
> The following are logs from Rgui.
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
> > ProjectPath<-"C:/ranger/Datasets/STarray/STarray -Project"
> > ArrayToolsPath<-"C:/Program Files (x86)/ArrayTools"
> > collationDataParam<-read.table(paste(ProjectPath,
> "/BinaryData/DataParam/collation.txt",sep=""),header=FALSE,sep="\t",
> fill=FALSE)
> > setwd(ProjectPath)
> >
> > #download cdf file from website
> >
> cdffileName<-as.character(unlist(strsplit(as.character(collationDataParam[which(collationDataParam[,2]=="s_cdfdownloadLink"),3]),"/"))[(length(unlist(strsplit(as.character(collationDataParam[which(collationDataParam[,2]=="s_cdfdownloadLink"),3]),"/"))))])
> >
> > #if (file.exists(paste(ArrayToolsPath,"/Misc/",cdffileName,sep=""))){
> > #createdTime<-file.info
> (paste(ArrayToolsPath,"/Misc/",cdffileName,sep=""))$ctime
> > #file.copy(paste(ArrayToolsPath,"/Misc/",cdffileName,sep="")
> >
> #,paste(ProjectPath,"/annotationData/chipTypes/",as.character(collationDataParam[which(collationDataParam[,2]=="s_Chiptype"),3]),"/",cdffileName,sep="")
> > #,overwrite = TRUE, recursive = FALSE)
> > #}else{
> >
> #download.file(url=as.character(collationDataParam[which(collationDataParam[,2]=="s_cdfdownloadLink"),3])
> > #,
> destfile=paste(ProjectPath,"/annotationData/chipTypes/",as.character(collationDataParam[which(collationDataParam[,2]=="s_Chiptype"),3]),"/",cdffileName,sep="")
> > #, method='internal',mode='wb')
> >
> #file.copy(paste(ProjectPath,"/annotationData/chipTypes/",as.character(collationDataParam[which(collationDataParam[,2]=="s_Chiptype"),3]),"/",cdffileName,sep="")
> > #,paste(ArrayToolsPath,"/Misc/",cdffileName,sep=""),overwrite = TRUE,
> recursive = FALSE)
> > #}
> >
> > #Qihao added the following codes to fix #452. 2/19/2013
> > source(paste(ArrayToolsPath,"/R/BiocUtil.r",sep=''))
> > if (!SetRPackageDir()) {
> + require(tcltk)
> + tkmessageBox(message="Writable R package directory cannot be
> found.",icon="error",type="ok")
> + print('Writable R package directory cannot be found when install
> aroma.affymetrix package',file=stderr())
> + return()
> + }
> >
> > local({r <- getOption('repos'); r['CRAN'] <- 'http://cran.r-project.org';
> options(repos=r)})
> > if (!any(installed.packages()[,1] == "aroma.affymetrix")){
> + source("http://aroma-project.org/hbLite.R";)
> + hbInstall("aroma.affymetrix")
> + }
> >
> > #Library
> > if (!any(installed.packages()[,1] ==
> "tcltk2")){install.packages("tcltk2", repos = "http://cran.r-project.org
> ")}
> > library('aroma.affymetrix')
> Loading required package: R.oo
> Loading required package: R.methodsS3
> R.methodsS3 v1.4.2 (2012-06-22) successfully loaded. See ?R.methodsS3 for
> help.
> R.oo v1.13.0 (2013-03-08) successfully loaded. See ?R.oo for help.
>
> Attaching package: ‘R.oo’
>
> The following object is masked from ‘package:methods’:
>
> getClasses, getMethods
>
> The following object is masked from ‘package:base’:
>
> attach, detach, gc, load, save
>
> Loading required package: R.utils
> R.utils v1.23.2 (2013-03-22) successfully loaded. See ?R.utils for help.
>
> Attaching package: ‘R.utils’
>
> The following object is masked from ‘package:utils’:
>
> timestamp
>
> The following object is masked from ‘package:base’:
>
> cat, commandArgs, getOption, inherits, isOpen, parse, warnings
>
> Loading required package: R.filesets
> R.filesets v2.0.1 (2013-03-04) successfully loaded. See ?R.filesets for
> help.
>
> Attaching package: ‘R.filesets’
>
> The following object is masked from ‘package:base’:
>
> append, readLines
>
> Loading required package: aroma.core
> Loading required package: R.devices
> R.devices v2.2.2 (2013-04-01) successfully loaded. See ?R.devices for help.
> Loading required package: R.rsp
> R.rsp v0.8.2 (2012-06-22) successfully loaded. See ?R.rsp for help.
> Type browseRsp() to open the RSP main menu in your browser.
>
> Attaching package: ‘R.rsp’
>
> The following object is masked from ‘package:R.filesets’:
>
> getHeader
>
> The following object is masked from ‘package:base’:
>
> flush, stop, write
>
> Loading required package: matrixStats
> matrixStats v0.8.1 (2013-05-02) successfully loaded. See ?matrixStats for
> help.
> aroma.core v2.9.5 (2013-05-30) successfully loaded. See ?aroma.core for
> help.
>
> Attaching package: ‘aroma.core’
>
> The following object is masked from ‘package:base’:
>
> .Machine, append, apply, colMeans, colSums, library, require
>
> Loading required package: aroma.light
> aroma.light v1.30.2 (2013-05-20) successfully loaded. See ?aroma.light for
> help.
>
> Attaching package: ‘aroma.light’
>
> The following object is masked from ‘package:aroma.core’:
>
> callNaiveGenotypes, normalizeTumorBoost
>
> Loading required package: aroma.apd
> Loading required package: R.huge
> R.huge v0.4.1 (2012-06-29) successfully loaded. See ?R.huge for help.
>
> Attaching package: ‘R.huge’
>
> The following object is masked from ‘package:aroma.core’:
>
> readHeader
>
> The following object is masked from ‘package:R.filesets’:
>
> getExtension, getFileSize, getPathname
>
> The following object is masked from ‘package:base’:
>
> colnames, flush, isOpen, ncol, nrow, rowMeans, rownames, rowSums
>
> Loading required package: affxparser
>
> Attaching package: ‘affxparser’
>
> The following object is masked from ‘package:R.utils’:
>
> findFiles
>
> aroma.apd v0.2.3 (2012-06-30) successfully loaded. See ?aroma.apd for help.
> aroma.affymetrix v2.9.4 (2013-05-30) successfully loaded. See
> ?aroma.affymetrix for help.
>
> Attaching package: ‘aroma.affymetrix’
>
> The following object is masked from ‘package:affxparser’:
>
> writeCdf
>
> The following object is masked from ‘package:base’:
>
> append, apply, colMeans, colSums, library, require
>
> > library('tcltk')
> > library('tcltk2')
>
> Attaching package: ‘tcltk2’
>
> The following object is masked from ‘package:R.rsp’:
>
> getLanguage
>
> >
> > if (file.exists(paste(ArrayToolsPath,"/Misc/",cdffileName,sep=""))){
> + file.copy(paste(ArrayToolsPath,"/Misc/",cdffileName,sep="")
> +
> ,paste(ProjectPath,"/annotationData/chipTypes/",as.character(collationDataParam[which(collationDataParam[,2]=="s_Chiptype"),3]),"/",cdffileName,sep="")
> + ,overwrite = TRUE, recursive = FALSE)
> + }else{
> + tkmessageBox(message="The CDF file had not been sucessfully downloaded.
> An error was occured.",icon='error')
> + print('The CDF file had not been sucessfully downloaded',file=stderr())
> + return()
> + }
> [1] TRUE
> >
> >
> >
> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> > chipType <-
> as.character(collationDataParam[which(collationDataParam[,2]=="s_Chiptype"),3])
> >
> cdfTag<-as.character(collationDataParam[which(collationDataParam[,2]=="s_cdfTag"),3])
> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTag)
> > print(cdf,file=stderr())
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuGene-1_0-st-v1
> Filename: HuGene-1_0-st-v1,r3.cdf
> File size: 16.67 MB (17476564 bytes)
> Chip type: HuGene-1_0-st-v1,r3
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 1050x1050
> Number of cells: 1102500
> Number of units: 33252
> Cells per unit: 33.16
> Number of QC units: 0
> > cs <- AffymetrixCelSet$byName("Dataset", cdf=cdf) # NOTE: This folder
> name, Dataset is hard coded!
> > print(cs,file=stderr())
> AffymetrixCelSet:
> Name: Dataset
> Tags:
> Path: rawData/Dataset/HuGene-1_0-st-v1
> Platform: Affymetrix
> Chip type: HuGene-1_0-st-v1,r3
> Number of arrays: 33
> Names: TisMap_Brain_01_v1_WTGene1, TisMap_Brain_02_v1_WTGene1,
> TisMap_Brain_03_v1_WTGene1, ..., TisMap_Thyroid_03_v1_WTGene1 [33]
> Time period: 2006-10-03 12:29:27 -- 2006-10-05 13:39:50
> Total file size: 349.21MB
> RAM: 0.04MB
> > setCdf(cs,cdf)
> > #Background Adjustment and Normalization
> > #In order to do RMA background correction, we setup a correction method
> and runs it by:
> > bc <- RmaBackgroundCorrection(cs, tag=unlist(strsplit(cdfTag,","))[1])
> > tk2<-tktoplevel()
> > tkwm.title(tk2,"Importering ST-Array into BRB-ArrayTools.")
> <Tcl>
> > progressbar<-tk2progress(tk2, orientation = "horizontal",
> mode="indeterminate", length=500,value=30)
> > tcl(progressbar, 'start')
> <Tcl> after#0
> > tkpack(progressbar)
> <Tcl>
> > tcl('wm', 'attributes', tk2$ID, '-topmost','1')
> <Tcl>
> > tkfocus(tk2)
> <Tcl>
> > csBC <- process(bc,verbose=verbose)
> 20130620 11:37:32|Background correcting data set...
> 20130620 11:37:34| Already background corrected
> 20130620 11:37:34|Background correcting data set...done
> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> > print(qn,file=stderr())
> QuantileNormalization:
> Data set: Dataset
> Input tags: r3
> User tags: *
> Asterisk ('*') tags: QN
> Output tags: r3,QN
> Number of files: 33 (346.99MB)
> Platform: Affymetrix
> Chip type: HuGene-1_0-st-v1,r3
> Algorithm parameters: {subsetToUpdate: NULL, typesToUpdate: chr "pm",
> subsetToAvg: NULL, typesToAvg: chr "pm", .targetDistribution: NULL}
> Output path: probeData/Dataset,r3,QN/HuGene-1_0-st-v1
> Is done: FALSE
> RAM: 0.00MB
> > csN <- process(qn, verbose=verbose)
> 20130620 11:37:55|Quantile normalizing data set...
> 20130620 11:37:55| Retrieving target distribution...
> 20130620 11:37:55| Getting target distribution...
> 20130620 11:37:55| Locating the target distribution file...
> 20130620 11:37:55| Root paths to be searched:
> [1] "probeData"
> 20130620 11:37:55| Subdirectories: Dataset,r3/HuGene-1_0-st-v1
> 20130620 11:37:55| Getting identifier for target distribution...
> Error in UseMethod("getChecksum") :
> no applicable method for 'getChecksum' applied to an object of class
> "list"
> 20130620 11:37:55| Getting identifier for target distribution...done
> 20130620 11:37:55| Locating the target distribution file...done
> 20130620 11:37:55| Getting target distribution...done
> 20130620 11:37:55| Retrieving target distribution...done
> 20130620 11:37:55|Quantile normalizing data set...done
> > traceback()
> 14: getChecksum(key)
> 13: getIdentifier.AffymetrixCelFile(X[[1L]], ...)
> 12: FUN(X[[1L]], ...)
> 11: lapply(this, FUN = getIdentifier)
> 10: getIdentifier.AffymetrixCelSet(ds)
> 9: getIdentifier(ds)
> 8: getTargetDistributionIdentifier.QuantileNormalization(this, verbose =
> less(verbose))
> 7: getTargetDistributionIdentifier(this, verbose = less(verbose))
> 6: findTargetDistributionFile.QuantileNormalization(this, verbose =
> less(verbose))
> 5: findTargetDistributionFile(this, verbose = less(verbose))
> 4: getTargetDistribution.QuantileNormalization(this, verbose =
> less(verbose))
> 3: getTargetDistribution(this, verbose = less(verbose))
> 2: process.QuantileNormalization(qn, verbose = verbose)
> 1: process(qn, verbose = verbose)
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] tcltk stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] tcltk2_1.2-5 aroma.affymetrix_2.9.4 affxparser_1.32.1
> aroma.apd_0.2.3 R.huge_0.4.1
> [6] aroma.light_1.30.2 aroma.core_2.9.5 matrixStats_0.8.1
> R.rsp_0.8.2 R.devices_2.2.2
> [11] R.filesets_2.0.1 R.utils_1.23.2 R.oo_1.13.0
> R.methodsS3_1.4.2
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.3 PSCBS_0.34.8 R.cache_0.6.5 tools_3.0.1
> >
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
> ---
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>
>
>
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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