Entering edit mode
Chao-Jen Wong
▴
580
@chao-jen-wong-3603
Last seen 10.0 years ago
USA/Seattle/Fred Hutchinson Cancer Reseā¦
Hi, Aric
We are able to reproduce the error using GvHD dataset. When setting
smooth=FALSE and using quadrantGate or quadGate as the filter, the
xyplot function would not work. There is certainly a bug in the
display
functions, and it is in our to-do list to fix it. I will let you know
as
soon as we fix it.
Thanks,
Chao-Jen
On 07/29/10 18:47, Aric Gregson wrote:
> Hello,
>
> I don't believe that I have seen an explanation and I suspect that I
am
> not calling the filter appropriately. Using flowStats in a workFlow
> with a quadrantGate making a filter I can easily plot the results
with
> the xyplot if smooth=TRUE (the default). However, when the
populations
> get small smooth=T is inadequate to visualize the results. Setting
> smooth=F results in:
>
> error in evaluating the argument 'subset' in selecting a method for
> 'Subset'
>
> quad <- quadrantGate(Data(wf[["CD4+CD3+"]]),
>
stains=c("Pacific.Blue.A","Alexa.Fluor.700.A"),
> plot=TRUE,
> filterId="quad",
> borderQuant=0.3,
> alpha=c(1,1),
> sd=c(0.6,0.6),
> refLine.1=5,
> refLine.2=5)
> add(wf, quad, parent="CD4+CD3+")
>
> -> This works fine:
> xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
> Data(wf[['CD4+CD3+']]),
> filter=quad)
>
> -> This fails with the above error message:
> xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
> Data(wf[['CD4+CD3+']]),
> smooth=F,
> filter=quad) -> I have tried to access gate, boundX/Y but not able
>
> This is consistent and can be replicated with the GvHD set using a
> similar filter setup.
>
> Thanks in advance.
> Aric
>
> sessionInfo()
> R version 2.11.0 (2010-04-22)
> amd64-portbld-freebsd8.1
>
> locale:
> [1] C
>
> attached base packages:
> [1] grid tools splines stats graphics grDevices
> utils [8] datasets methods base
>
> other attached packages:
> [1] Rgraphviz_1.26.0 graph_1.26.0 flowQ_1.9.0
> [4] latticeExtra_0.6-11 RColorBrewer_1.0-2 parody_1.6.0
> [7] bioDist_1.20.0 KernSmooth_2.23-3 outliers_0.13-2
> [10] flowStats_1.7.5 cluster_1.12.3 mvoutlier_1.4
> [13] fda_2.2.2 zoo_1.6-4 flowViz_1.13.1
> [16] lattice_0.18-5 flowCore_1.15.2 rrcov_1.0-01
> [19] pcaPP_1.8-2 mvtnorm_0.9-92 robustbase_0.5-0-1
> [22] Biobase_2.8.0 fortunes_1.3-7
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.10.2 DBI_0.2-5 MASS_7.3-5
> [4] RSQLite_0.9-2 annotate_1.26.1 feature_1.2.4
> [7] geneplotter_1.26.0 ks_1.6.13 stats4_2.11.0
> [10] xtable_1.5-6
>
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>
--
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org