Hi Dan,

Thank you very much for the detail explanation. I agree it is better to wait for the new version.

I saw the new version 1.4.1 was released now. However, it seems couldn't be downloaded.

Thanks,

Li


> source("http://bioconductor.org/biocLite.R")

> biocLite("inSilicoMerging")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
Installing package(s) 'inSilicoMerging'
trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/inSilicoMerging_1.4.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/inSilicoMerging_1.4.0.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘inSilicoMerging’ failed

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

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

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

other attached packages:
[1] Biobase_2.20.1       BiocGenerics_0.6.0   BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] affy_1.38.1           affyio_1.28.0         MASS_7.3-28           preprocessCore_1.22.0 tools_3.0.1          
[6] zlibbioc_1.6.0       

> Date: Wed, 7 Aug 2013 16:04:04 -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 3:47 PM, Li Liu <liliu_1@hotmail.com> wrote:
> > 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?
> >
> 
> 
> Actually, I don't think installing this old tarball of DWD will work
> for you as it is a source tarball and requires a C compiler and other
> tools to be installed in a very specific way.
> 
> I recommend either (1) waiting till tomorrow, (2) installing the
> latest version of inSilicoMerging via Subversion, or (3) making the
> change yourself.
> 
> To do (2), you need Subversion installed, see
> http://www.bioconductor.org/developers/how-to/source-control/
> for more information.
> You would do this:
> 
> svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/inSilicoMerging/
> R CMD INSTALL inSilicoMerging
> 
> To do (3), download the package from
> http://www.bioconductor.org/packages/release/bioc/src/contrib/inSilicoMerging_1.4.0.tar.gz
> 
> Then open a command shell and navigate to the directory where the file
> was downloaded.
> Then uncompress the file, the usual way is
> tar zxf InsilicoMerging_1.4.0.tar.gz
> but if you don't have the tar command installed, you'll need to figure
> out another way to do this. There are graphical programs available for
> windows that will do this.
> 
> You will end up with an
> InsilicoMerging
> directory.
> Edit two files in that directory:
> 
> edit DESCRIPTION and change the line
> Version: 1.4.0
> to
> Version: 1.4.1
> 
> and edit R/dwd.R and change line 9 from this:
> 
>   res = kdwd(x=t(exprs(eset)), y=batchInfo, scaled=FALSE);
> 
> to this:
> 
>   res = kdwd(x=t(exprs(eset)), y=as.factor(batchInfo), scaled=FALSE);
> 
> 
> Then, still in the command window, do this:
> R CMD INSTALL InSilicoMerging
> 
> If that all seems like too much work, I again recommend waiting until tomorrow.
> 
> Dan
> 
> 

 		 	   		  
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