Hi Dan, 

Thank you very much for the reply.

I try to install the old version of DWD so I don't need to wait for tomorrow's new version. However I am not quite familiar the installation. After download should I put the compressed file "DWD_0.10.tar.gz" in a specific folder or I should unzipped it first?

Here is what I got in R after download the file and run install.packages.

Many thanks,

Li


> install.packages("DWD_0.10.tar.gz", repos=NULL, type="source")
Warning in install.packages :
  package İoWD_0.10.tar.gz?is not available (for R version 3.0.1)
Installing package into ·Y:/Users/lucy/Documents/R/win-library/3.0?(as áÌib?is unspecified)
Warning: invalid package 'DWD_0.10.tar.gz'
Error: ERROR: no packages specified
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-30~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\lucy\Documents\R\win-library\3.0" "DWD_0.10.tar.gz"' had status 1
Warning in install.packages :
  installation of package İoWD_0.10.tar.gz?had non-zero exit status
Warning message:
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated") 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] inSilicoMerging_1.4.0 DWD_0.11              Matrix_1.0-12        
[4] lattice_0.20-15       hgu133acdf_2.12.0     AnnotationDbi_1.22.6 
[7] affy_1.38.1           Biobase_2.20.1        BiocGenerics_0.6.0   

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         BiocInstaller_1.10.3  DBI_0.2-7            
 [4] grid_3.0.1            IRanges_1.18.2        preprocessCore_1.22.0
 [7] RSQLite_0.11.4        stats4_3.0.1          tools_3.0.1          
[10] zlibbioc_1.6.0       


> Date: Wed, 7 Aug 2013 11:37:49 -0700
> Subject: Re: [BioC] DWD method for batch effect removal
> From: dtenenba@fhcrc.org
> To: liliu_1@hotmail.com
> CC: bioconductor@r-project.org; jtaminau@vub.ac.be; smeganck@vub.ac.be
> 
> On Wed, Aug 7, 2013 at 11:04 AM, Li Liu <liliu_1@hotmail.com> wrote:
> > HI,
> >
> > I am using inSilicoMerging package to remove batch effect. A few merging methods, such as  COMBAT, BMC, GENENORM, work well for me, so I suppose my dataset has no problem. However, when I use the method DWD, there is an error
> > Error in is.factor(x) : object 'ybuf' not found
> >  Is there anybody who can help this?
> >
> 
> Seems like the problem is upstream in the DWD package. I've sent an
> email with a bug report to the DWD maintainer. The problem seems
> easily fixable. A workaround is to install an older version of DWD
> from here:
> 
> http://cran.r-project.org/src/contrib/Archive/DWD/DWD_0.10.tar.gz
> 
> After downloading, you can install on the command line with
> R CMD INSTALL DWD_0.10.tar.gz
> or within R:
> 
> install.packages("DWD_0.10.tar.gz", repos=NULL, type="source")
> 
> Dan
> 
> 
> 
> > Thanks.
> >
> > Li
> >
> >
> >
> >> esets=list(eset1, eset2, eset3, eset4, eset5, eset6)
> >
> >> # Merge esets by different methods
> >
> >> library(inSilicoMerging)
> > Loading required package: DWD
> > Loading required package: Matrix
> > Loading required package: lattice
> >
> >
> >> eset_NONE=merge(esets, method='NONE')
> >   INSILICOMERGING: Run NONE...
> >
> >> eset_BMC=merge(esets, method='BMC')
> >   INSILICOMERGING: Run BMC...
> >
> >> eset_COMBAT=merge(esets, method='COMBAT')
> >   INSILICOMERGING: Run COMBAT...
> >   INSILICOMERGING:   => Found 6 batches
> >   INSILICOMERGING:   => Found 0 covariate(s)
> >
> >> eset_GENENORM=merge(esets, method='GENENORM')
> >   INSILICOMERGING: Run GENENORM...
> >
> >> eset_DWD=merge(esets, method='DWD')
> >   INSILICOMERGING: Run DWD...
> > Error in is.factor(x) : object 'ybuf' not found
> >
> >> sessionInfo()
> > R version 3.0.1 (2013-05-16)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
> > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> > [5] LC_TIME=English_Canada.1252
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] inSilicoMerging_1.4.0 DWD_0.11              Matrix_1.0-12
> > [4] lattice_0.20-15       hgu133acdf_2.12.0     AnnotationDbi_1.22.6
> > [7] affy_1.38.1           Biobase_2.20.1        BiocGenerics_0.6.0
> >
> > loaded via a namespace (and not attached):
> >  [1] affyio_1.28.0         BiocInstaller_1.10.3  DBI_0.2-7
> >  [4] grid_3.0.1            IRanges_1.18.2        preprocessCore_1.22.0
> >  [7] RSQLite_0.11.4        stats4_3.0.1          tools_3.0.1
> > [10] zlibbioc_1.6.0
> >
> >         [[alternative HTML version deleted]]
> >
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