Re: [aroma.affymetrix] Error in UseMethod(getChecksum) when processing Affymetrix Human Gene 1.0 ST arrays

2013-06-26 Thread Henrik Bengtsson 
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:

[aroma.affymetrix] Error in UseMethod(getChecksum) when processing Affymetrix Human Gene 1.0 ST arrays

2013-06-20 Thread rangerq 
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

Re: [aroma.affymetrix] Error in UseMethod(getChecksum) when processing Affymetrix Human Gene 1.0 ST arrays

2013-06-20 Thread Henrik Bengtsson 
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