[BioC] DWD method for batch effect removal

[Dan Tenenbaum]

On Thu, Aug 8, 2013 at 10:51 AM, Li Liu <liliu_1 at hotmail.com> wrote:
> 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.
>

I was just able to install it on windows in BioC 2.12.

Try again with a fresh R session.

Dan


> 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 at fhcrc.org
>> To: liliu_1 at hotmail.com
>> CC: bioconductor at r-project.org; jtaminau at vub.ac.be; smeganck at vub.ac.be
>>
>> On Wed, Aug 7, 2013 at 3:47 PM, Li Liu <liliu_1 at 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
>>
>>
>