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

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

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 > >