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
>
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