[BioC] flowStats's warping function problem
Chao-Jen Wong
cwon2 at fhcrc.org
Mon Oct 12 23:11:08 CEST 2009
Sorry, forget to attach my sessionInfo. Please notice that I use
fda_2.1.3 instead of fda2.1.2
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-11 r49665)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] flowViz_1.9.9 lattice_0.17-25 flowStats_1.3.6 fda_2.1.3
[5] zoo_1.5-6 flowCore_1.11.19 rrcov_0.5-01 pcaPP_1.6
[9] mvtnorm_0.9-7 robustbase_0.4-5 Biobase_2.5.8
loaded via a namespace (and not attached):
[1] KernSmooth_2.23-3 MASS_7.3-2 RColorBrewer_1.0-2 feature_1.2.3
[5] graph_1.23.2 grid_2.10.0 ks_1.6.5
latticeExtra_0.6-1
[9] stats4_2.10.0 tools_2.10.0
Chao-Jen Wong wrote:
> Hi, Josef,
>
> As for the second issue that you mentioned (below), since warpSet itself
> returns a flowSet object, it makes sense warpSet(original,
> "FL1-H")$flowset would return NULL (see the value section in warpSet's
> man page). The correct way is to get the resulting flowSet object is:
> obj <- warpSet(original, "FL1-H")
> str(obj)
>
> To view the result, do
> densityplot(~`FL1-H`, original)
>
> Sorry for the delay of my response.
>
> Cheers,
> Chao-Jen
>
>>>> Issue 2, no error but returns NULL:
>>>> > warpSet(original, "FL1-H")$flowset
>>>> Estimating landmarks for channel FL1-H ...
>>>> Registering curves for parameter FL1-H ...
>>>> NULL
>>>> >
>>>>
>
>
--
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org
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