Question: FW: DWD method for batch effect removal
0
gravatar for Li Liu
5.9 years ago by
Li Liu100
Canada
Li Liu100 wrote:
From: liliu_1@hotmail.com To: dtenenba@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. :( Thanks again and you are always helpful. Li On Aug 2, 2013 9:23 AM, "Li Liu" <liliu_1@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@fhcrc.org > To: liliu_1@hotmail.com > CC: bioconductor@r-project.org; jtaminau@vub.ac.be; smeganck@vub.ac.be > > On Thu, Aug 8, 2013 at 10:51 AM, Li Liu <liliu_1@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]]
• 526 views
ADD COMMENTlink modified 5.9 years ago by Dan Tenenbaum8.2k • written 5.9 years ago by Li Liu100
Answer: FW: DWD method for batch effect removal
0
gravatar for Dan Tenenbaum
5.9 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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
ADD COMMENTlink written 5.9 years ago by Dan Tenenbaum8.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 505 users visited in the last hour