Question: DWD method for batch effect removal
0
gravatar for Li Liu
5.6 years ago by
Li Liu100
Canada
Li Liu100 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? 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]]
insilicomerging • 1.3k views
ADD COMMENTlink modified 5.6 years ago by Dan Tenenbaum8.2k • written 5.6 years ago by Li Liu100
Answer: DWD method for batch effect removal
0
gravatar for Dan Tenenbaum
5.6 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Wed, Aug 7, 2013 at 11:04 AM, Li Liu <liliu_1 at="" 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]] > > _______________________________________________ > 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 5.6 years ago by Dan Tenenbaum8.2k
On Wed, Aug 7, 2013 at 11:37 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Wed, Aug 7, 2013 at 11:04 AM, Li Liu <liliu_1 at="" 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? >> I've checked version 1.4.1 of inSilicoMerging which contains a workaround for this problem. It will be available tomorrow around 10:30AM Seattle time (or now via svn). Devel version has been fixed as well. Thanks, Dan > > 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]] >> >> _______________________________________________ >> 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 REPLYlink written 5.6 years ago by Dan Tenenbaum8.2k
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 ÝoWD_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 ÝoWD_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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by Li Liu100
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/m adman/Rpacks/inSilicoMerging/ R CMD INSTALL inSilicoMerging To do (3), download the package from http://www.bioconductor.org/packages/release/bioc/src/contrib/inSilico Merging_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 > 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 ?WD_0.10.tar.gz?is not available (for R version 3.0.1) > Installing package into ?:/Users/lucy/Documents/R/win- library/3.0?(as ?ib?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 ?WD_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 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 11:04 AM, Li Liu <liliu_1 at="" 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]] >> > >> > _______________________________________________ >> > 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 REPLYlink written 5.6 years ago by Dan Tenenbaum8.2k
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/con trib/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/wind ows/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/inSili coMerging_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 > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by Li Liu100
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/madma n/Rpacks/inSilicoMerging/ >> R CMD INSTALL inSilicoMerging >> >> To do (3), download the package from >> >> http://www.bioconductor.org/packages/release/bioc/src/contrib/inSil icoMerging_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 >> >> >
ADD REPLYlink written 5.6 years ago by Dan Tenenbaum8.2k
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