Search
Question: help with flowQ vignette
0
gravatar for Frederico Moraes Ferreira
4.9 years ago by
Brazil
Hi List, I'm following the flowQ vignette (DataQualityAssessment.R) and get stucked in the transformation bellow. I've check manuals, google and ?transformList and can't figure out what's wrong. Please, could someone give me a hand? > load("qData.rda") > qData[[1]][[1]] flowFrame object 'pid02050' with 4500 cells and 8 observables: name desc range minRange maxRange $P1 FSC-A FSC-A 1024 0 1023 $P2 SSC-A SSC-A 1024 0 1023 $P3 FITC-A CD45RA 1024 1 10000 $P4 PE-A CD45RO 1024 1 10000 $P5 FL3-A CD8 1024 1 10000 $P6 PE-Cy7-A CD4 1024 1 10000 $P7 APC-A CD62L 1024 1 10000 $P8 Time <na> 1024 0 1023 82 keywords are stored in the 'description' slot > tData <- lapply(qData, function(x) transformList(colnames(x)[3:7], asinh) %on% x) Error in FUN(X[[1L]], ...) : could not find function "%on%" > R.version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 3 minor 0.0 year 2013 month 04 day 03 svn rev 62481 language R version.string R version 3.0.0 (2013-04-03) nickname Masked Marvel > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0. Best, -- Dr. Frederico Moraes Ferreira University of Sao Paulo Heart Institute, School of Medicine Laboratoy of Immunology Av. Dr. En?as de Carvalho Aguiar, 44 05403-900 Sao Paulo - SP Brasil
ADD COMMENTlink modified 4.9 years ago by Dan Tenenbaum ♦♦ 8.2k • written 4.9 years ago by Frederico Moraes Ferreira100
0
gravatar for Dan Tenenbaum
4.9 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
Hi Frederico, On Tue, May 14, 2013 at 11:22 AM, Frederico Moraes Ferreira <ferreirafm at="" usp.br=""> wrote: > Hi List, > I'm following the flowQ vignette (DataQualityAssessment.R) and get stucked > in the transformation bellow. > I've check manuals, google and ?transformList and can't figure out what's > wrong. > Please, could someone give me a hand? > >> load("qData.rda") >> qData[[1]][[1]] > flowFrame object 'pid02050' > with 4500 cells and 8 observables: > name desc range minRange maxRange > $P1 FSC-A FSC-A 1024 0 1023 > $P2 SSC-A SSC-A 1024 0 1023 > $P3 FITC-A CD45RA 1024 1 10000 > $P4 PE-A CD45RO 1024 1 10000 > $P5 FL3-A CD8 1024 1 10000 > $P6 PE-Cy7-A CD4 1024 1 10000 > $P7 APC-A CD62L 1024 1 10000 > $P8 Time <na> 1024 0 1023 > 82 keywords are stored in the 'description' slot >> tData <- lapply(qData, function(x) transformList(colnames(x)[3:7], asinh) >> %on% x) > Error in FUN(X[[1L]], ...) : could not find function "%on%" This command works for me. Can you send the output of the sessionInfo() command (after loading flowQ)? That will help us figure out the problem. Thanks, Dan >> R.version > _ > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 3 > minor 0.0 > year 2013 > month 04 > day 03 > svn rev 62481 > language R > version.string R version 3.0.0 (2013-04-03) > nickname Masked Marvel >> biocLite() > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0. > > > > > Best, > > -- > Dr. Frederico Moraes Ferreira > University of Sao Paulo > Heart Institute, School of Medicine > Laboratoy of Immunology > Av. Dr. En?as de Carvalho Aguiar, 44 > 05403-900 Sao Paulo - SP > Brasil > > _______________________________________________ > 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 4.9 years ago by Dan Tenenbaum ♦♦ 8.2k
Hi Dan, Thanks for answer. The problem has been solved loading flowQ again. Perhaps, that's happened because I was working on a "Previously saved workspace restored". My current sessionInfo() is as follows: > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] grid splines tools parallel stats graphics grDevices [8] utils datasets methods base other attached packages: [1] flowStats_1.18.0 flowWorkspace_1.6.0 ncdfFlow_1.6.0 [4] Rgraphviz_2.4.0 gridExtra_0.9.1 hexbin_1.26.2 [7] IDPmisc_1.1.17 XML_3.96-1.1 RBGL_1.36.2 [10] graph_1.38.0 Cairo_1.5-2 Rcpp_0.10.3 [13] cluster_1.14.4 fda_2.3.4 Matrix_1.0-12 [16] zoo_1.7-9 flowQ_1.20.0 latticeExtra_0.6-24 [19] RColorBrewer_1.0-5 parody_1.18.0 bioDist_1.32.0 [22] KernSmooth_2.23-10 mvoutlier_1.9.9 sgeostat_1.0-25 [25] robCompositions_1.6.3 car_2.0-17 nnet_7.3-6 [28] compositions_1.30-1 energy_1.6.0 MASS_7.3-26 [31] boot_1.3-9 tensorA_0.36 rgl_0.93.935 [34] flowViz_1.24.0 flowCore_1.26.0 rrcov_1.3-3 [37] pcaPP_1.9-49 mvtnorm_0.9-9994 robustbase_0.9-7 [40] Biobase_2.20.0 lattice_0.20-15 outliers_0.14 [43] BiocGenerics_0.6.0 BiocInstaller_1.10.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.22.5 DBI_0.2-7 IRanges_1.18.1 [4] RSQLite_0.11.3 annotate_1.38.0 feature_1.2.8 [7] geneplotter_1.38.0 ks_1.8.12 stats4_3.0.0 [10] xtable_1.7-1 Best, -- Dr. Frederico Moraes Ferreira University of Sao Paulo Heart Institute, School of Medicine Laboratoy of Immunology Av. Dr. En?as de Carvalho Aguiar, 44 05403-900 Sao Paulo - SP Brasil Em 14-05-2013 15:35, Dan Tenenbaum escreveu: > Hi Frederico, > > > > On Tue, May 14, 2013 at 11:22 AM, Frederico Moraes Ferreira > <ferreirafm at="" usp.br=""> wrote: >> Hi List, >> I'm following the flowQ vignette (DataQualityAssessment.R) and get stucked >> in the transformation bellow. >> I've check manuals, google and ?transformList and can't figure out what's >> wrong. >> Please, could someone give me a hand? >> >>> load("qData.rda") >>> qData[[1]][[1]] >> flowFrame object 'pid02050' >> with 4500 cells and 8 observables: >> name desc range minRange maxRange >> $P1 FSC-A FSC-A 1024 0 1023 >> $P2 SSC-A SSC-A 1024 0 1023 >> $P3 FITC-A CD45RA 1024 1 10000 >> $P4 PE-A CD45RO 1024 1 10000 >> $P5 FL3-A CD8 1024 1 10000 >> $P6 PE-Cy7-A CD4 1024 1 10000 >> $P7 APC-A CD62L 1024 1 10000 >> $P8 Time <na> 1024 0 1023 >> 82 keywords are stored in the 'description' slot >>> tData <- lapply(qData, function(x) transformList(colnames(x)[3:7], asinh) >>> %on% x) >> Error in FUN(X[[1L]], ...) : could not find function "%on%" > This command works for me. Can you send the output of the > sessionInfo() command (after loading flowQ)? That will help us figure > out the problem. > > Thanks, > Dan > > >>> R.version >> _ >> platform x86_64-pc-linux-gnu >> arch x86_64 >> os linux-gnu >> system x86_64, linux-gnu >> status >> major 3 >> minor 0.0 >> year 2013 >> month 04 >> day 03 >> svn rev 62481 >> language R >> version.string R version 3.0.0 (2013-04-03) >> nickname Masked Marvel >>> biocLite() >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0. >> >> >> >> >> Best, >> >> -- >> Dr. Frederico Moraes Ferreira >> University of Sao Paulo >> Heart Institute, School of Medicine >> Laboratoy of Immunology >> Av. Dr. En?as de Carvalho Aguiar, 44 >> 05403-900 Sao Paulo - SP >> Brasil >> >> _______________________________________________ >> 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 4.9 years ago by Frederico Moraes Ferreira100
0
gravatar for Dan Tenenbaum
4.9 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
Hi Frederico, On Tue, May 14, 2013 at 12:05 PM, Frederico Moraes Ferreira <ferreirafm at="" usp.br=""> wrote: > Hi Dan, > Thanks for answer. The problem has been solved loading flowQ again. > Perhaps, that's happened because I was working on a " Previously saved > workspace restored". Glad to know the problem is solved. CC'ing the Bioconductor list in case this helps others. Dan > My current sessionInfo() is as follows: > > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid splines tools parallel stats graphics grDevices > [8] utils datasets methods base > > other attached packages: > [1] flowStats_1.18.0 flowWorkspace_1.6.0 ncdfFlow_1.6.0 > [4] Rgraphviz_2.4.0 gridExtra_0.9.1 hexbin_1.26.2 > [7] IDPmisc_1.1.17 XML_3.96-1.1 RBGL_1.36.2 > [10] graph_1.38.0 Cairo_1.5-2 Rcpp_0.10.3 > [13] cluster_1.14.4 fda_2.3.4 Matrix_1.0-12 > [16] zoo_1.7-9 flowQ_1.20.0 latticeExtra_0.6-24 > [19] RColorBrewer_1.0-5 parody_1.18.0 bioDist_1.32.0 > [22] KernSmooth_2.23-10 mvoutlier_1.9.9 sgeostat_1.0-25 > [25] robCompositions_1.6.3 car_2.0-17 nnet_7.3-6 > [28] compositions_1.30-1 energy_1.6.0 MASS_7.3-26 > [31] boot_1.3-9 tensorA_0.36 rgl_0.93.935 > [34] flowViz_1.24.0 flowCore_1.26.0 rrcov_1.3-3 > [37] pcaPP_1.9-49 mvtnorm_0.9-9994 robustbase_0.9-7 > [40] Biobase_2.20.0 lattice_0.20-15 outliers_0.14 > [43] BiocGenerics_0.6.0 BiocInstaller_1.10.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.22.5 DBI_0.2-7 IRanges_1.18.1 > [4] RSQLite_0.11.3 annotate_1.38.0 feature_1.2.8 > [7] geneplotter_1.38.0 ks_1.8.12 stats4_3.0.0 > [10] xtable_1.7-1 > > > Best, > > -- > Dr. Frederico Moraes Ferreira > University of Sao Paulo > Heart Institute, School of Medicine > Laboratoy of Immunology > Av. Dr. En?as de Carvalho Aguiar, 44 > 05403-900 Sao Paulo - SP > Brasil > > > > Em 14-05-2013 15:35, Dan Tenenbaum escreveu: > >> Hi Frederico, >> >> >> >> On Tue, May 14, 2013 at 11:22 AM, Frederico Moraes Ferreira >> <ferreirafm at="" usp.br=""> wrote: >>> >>> Hi List, >>> I'm following the flowQ vignette (DataQualityAssessment.R) and get >>> stucked >>> in the transformation bellow. >>> I've check manuals, google and ?transformList and can't figure out what's >>> wrong. >>> Please, could someone give me a hand? >>> >>>> load("qData.rda") >>>> qData[[1]][[1]] >>> >>> flowFrame object 'pid02050' >>> with 4500 cells and 8 observables: >>> name desc range minRange maxRange >>> $P1 FSC-A FSC-A 1024 0 1023 >>> $P2 SSC-A SSC-A 1024 0 1023 >>> $P3 FITC-A CD45RA 1024 1 10000 >>> $P4 PE-A CD45RO 1024 1 10000 >>> $P5 FL3-A CD8 1024 1 10000 >>> $P6 PE-Cy7-A CD4 1024 1 10000 >>> $P7 APC-A CD62L 1024 1 10000 >>> $P8 Time <na> 1024 0 1023 >>> 82 keywords are stored in the 'description' slot >>>> >>>> tData <- lapply(qData, function(x) transformList(colnames(x)[3:7], >>>> asinh) >>>> %on% x) >>> >>> Error in FUN(X[[1L]], ...) : could not find function "%on%" >> >> This command works for me. Can you send the output of the >> sessionInfo() command (after loading flowQ)? That will help us figure >> out the problem. >> >> Thanks, >> Dan >> >> >>>> R.version >>> >>> _ >>> platform x86_64-pc-linux-gnu >>> arch x86_64 >>> os linux-gnu >>> system x86_64, linux-gnu >>> status >>> major 3 >>> minor 0.0 >>> year 2013 >>> month 04 >>> day 03 >>> svn rev 62481 >>> language R >>> version.string R version 3.0.0 (2013-04-03) >>> nickname Masked Marvel >>>> >>>> biocLite() >>> >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0. >>> >>> >>> >>> >>> Best, >>> >>> -- >>> Dr. Frederico Moraes Ferreira >>> University of Sao Paulo >>> Heart Institute, School of Medicine >>> Laboratoy of Immunology >>> Av. Dr. En?as de Carvalho Aguiar, 44 >>> 05403-900 Sao Paulo - SP >>> Brasil >>> >>> _______________________________________________ >>> 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 4.9 years ago by Dan Tenenbaum ♦♦ 8.2k
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 2.2.0
Traffic: 187 users visited in the last hour