Thanks both for the report and follow up. I've updated
aroma.affymetrix (v2.9.5) as well (previously only aroma.core) for
this. Install as usual:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Let me know if this solves your problem.
/Henrik
On Wed, Jun 26, 2013 at 5:54 AM, ying chen <njs...@gmail.com> wrote:
> Hi Henrik,
>
> I got the same Error in UseMethod("getChecksum") error message when
> processing U133Plus2 chips even after I loaded R.cache at startup. Any
> suggestion?
>
> Thanks a lot for the help!
>
> Ying
>
>> library(R.cache)
> Loading required package: R.utils
>
> 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
> 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
> R.cache v0.6.5 (2012-11-18) successfully loaded. See ?R.cache for help.
>> library(aroma.affymetrix)
>
> 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:R.cache’:
> getChecksum
> 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
>> ces <- doRMA("MYgastric", chipType="HG-U133_Plus_2,Binary,Hs_ENTREZG",
>> verbose=-5)
> RMA...
> RMA/Setting up CEL set...
> AffymetrixCelSet:
> Name: MYgastric
> Tags:
> Path: rawData/MYgastric/HG-U133_Plus_2
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2,Binary,Hs_ENTREZG
> Number of arrays: 400
> Names: 107T, 108T, 109T, ..., Tr_97 [400]
> Time period: 2012-03-08 16:25:16 -- 2012-09-26 21:47:21
> Total file size: 5175.22MB
> RAM: 0.46MB
> RMA/Setting up CEL set...done
> RMA...
> Arguments:
> arrays:
> chr ""
> Fit PLM on unique probe sets: FALSE
> Data set
> AffymetrixCelSet:
> Name: MYgastric
> Tags:
> Path: rawData/MYgastric/HG-U133_Plus_2
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2,Binary,Hs_ENTREZG
> Number of arrays: 400
> Names: 107T, 108T, 109T, ..., Tr_97 [400]
> Time period: 2012-03-08 16:25:16 -- 2012-09-26 21:47:21
> Total file size: 5175.22MB
> RAM: 0.46MB
> Checking whether final results are available or not...
> Checking whether final results are available or not...done
> RMA/Background correction (normal & exponential mixture model)...
> RmaBackgroundCorrection:
> Data set: MYgastric
> Input tags:
> User tags: *
> Asterisk ('*') tags: RBC
> Output tags: RBC
> Number of files: 400 (5175.22MB)
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2,Binary,Hs_ENTREZG
> Algorithm parameters: {subsetToUpdate: NULL, typesToUpdate: chr "pm",
> addJitter: logi FALSE, jitterSd: num 0.2, pmonly: logi TRUE}
> Output path: probeData/MYgastric,RBC/HG-U133_Plus_2
>
> Is done: FALSE
> RAM: 0.00MB
> Background correcting data set...
> Number of arrays: 400
> Array #1 ('107T') of 400...
> Loading required package: affy
> Loading required package: BiocGenerics
> Loading required package: parallel
> Attaching package: ‘BiocGenerics’
> The following objects are masked from ‘package:parallel’:
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
> clusterMap, parApply, parCapply,
> parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
> The following object is masked from ‘package:R.huge’:
> colnames, rownames
> The following object is masked from ‘package:stats’:
> xtabs
> The following objects are masked from ‘package:base’:
> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter,
> Find, get, intersect, lapply, Map,
> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> Position, rank, rbind, Reduce, rep.int,
> rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
> Loading required package: Biobase
> Welcome to Bioconductor
> Vignettes contain introductory material; view with 'browseVignettes()'.
> To cite Bioconductor, see
> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Attaching package: ‘Biobase’
> The following object is masked from ‘package:matrixStats’:
> anyMissing, rowMedians
>
> Attaching package: ‘affy’
> The following object is masked from ‘package:aroma.light’:
> plotDensity
> The following object is masked _by_ package:Biobase:
> .Depends, exprs, featureNames, sampleNames, se.exprs, show, updateObject
> The following object is masked _by_ package:BiocGenerics:
> .Depends, boxplot, image, updateObject
> The following object is masked _by_ package:aroma.affymetrix:
> .Depends
> The following object is masked _by_ package:aroma.apd:
> .Depends
> The following object is masked _by_ package:R.huge:
> .Depends, close, open
> The following object is masked _by_ package:aroma.light:
> .Depends, plotDensity
> The following object is masked _by_ package:aroma.core:
> .Depends
> The following object is masked _by_ package:R.rsp:
> .Depends
> The following object is masked _by_ package:R.devices:
> .Depends
> The following object is masked _by_ package:R.filesets:
> .Depends
> The following object is masked _by_ package:R.cache:
> .Depends
> The following object is masked _by_ package:R.utils:
> .Depends
> The following object is masked _by_ package:R.oo:
> .Depends
> The following object is masked from package:graphics:
> barplot, boxplot, hist, image
> The following object is masked from package:methods:
> show
> The following object is masked from package:base:
> close, open
> Adjusting PM signals only
> Obtaining signals...
>
> Error in UseMethod("getChecksum") :
> no applicable method for 'getChecksum' applied to an object of class
> "list"
> In addition: Warning message:
> In fcn(...) : Packages reordered in search path: package:affy
> Obtaining signals...done
> Array #1 ('107T') of 400...done
> Background correcting data set...done
>>
>> 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] parallel stats graphics grDevices utils datasets methods
> base
> other attached packages:
> [1] Biobase_2.20.0 BiocGenerics_0.6.0 aroma.affymetrix_2.9.4
> affxparser_1.32.1 aroma.apd_0.2.3
> [6] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2.9.5
> matrixStats_0.8.1 R.rsp_0.8.2
> [11] R.devices_2.2.2 R.filesets_2.0.1 R.cache_0.6.5
> R.utils_1.23.2 R.oo_1.13.0
> [16] affy_1.38.1 R.methodsS3_1.4.2
> loaded via a namespace (and not attached):
> [1] affyio_1.28.0 BiocInstaller_1.10.2 digest_0.6.3
> preprocessCore_1.22.0 PSCBS_0.34.8
> [6] zlibbioc_1.6.0
>>
>
>
>
> On Thu, Jun 20, 2013 at 2:29 PM, Henrik Bengtsson
> <henrik.bengts...@gmail.com> wrote:
>>
>> 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/
>>>
>>> ---
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to aroma-affymetrix+unsubscr...@googlegroups.com.
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>>
>>
>> --
>> --
>> 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/
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to aroma-affymetrix+unsubscr...@googlegroups.com.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
--
--
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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