[BioC] FW: DWD method for batch effect removal

[Dan Tenenbaum]

On Thu, Aug 8, 2013 at 11:56 AM, Li Liu <liliu_1 at hotmail.com> wrote:
>
>
> From: liliu_1 at hotmail.com
> To: dtenenba at fhcrc.org
> Subject: RE: [BioC] DWD method for batch effect removal
> Date: Thu, 8 Aug 2013 14:55:59 -0400
>
>
>
>
> Hi Dan,
>
> Thank you very much. It works well now. Exciting! :)
>
> Now the only concern about this package is the new version still doesn't have those functions which were in the version 1.2.3 as I asked in another day. :(
>

Looks like those functions were added in a previous release branch of
Subversion so did not propagate into future versions of BioC. This was
probably not the package maintainers' intention. I will contact them
about this.

Dan


> Thanks again and you are always helpful.
>
> Li
>
>
> On Aug 2, 2013 9:23 AM, "Li Liu" <liliu_1 at hotmail.com> wrote:
>
> Hi,
>
>
>
> I am new for R and Bioconductor. I want to use Bioconductor inSilicoMerging package to study batch effects.
>
>
>
> When I check from internet I found the package contains the functions of
>
>
>
> measureAsymmetry
>
> measureGenesMeanCorrCoef
>
> measureGenesOverlap
>
> measureSamplesMeanCorrCoef
>
> measureSamplesOverlap
>
>
>
> These functions can be used to evaluate batch effect removal methods.
> However, the current version of the package doesn't include these
> functions and some plot functions were also removed. I wondering whether
>  these functions had been moved to other packages.
>
>
>
>
> It is great appreciate if anyone can help.
>
>
>
> Thanks,
>
>
>
>
>> Date: Thu, 8 Aug 2013 10:53:26 -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 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
>>
>>
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor