[BioC] help with flowQ vignette

[Dan Tenenbaum]

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. 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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>
>