[BioC] help with flowQ vignette
Frederico Moraes Ferreira
ferreirafm at usp.br
Tue May 14 21:12:49 CEST 2013
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. Enéas 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. Enéas de Carvalho Aguiar, 44
>> 05403-900 Sao Paulo - SP
>> Brasil
>>
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