[BioC] Help Understand flowViz Error
Nishant Gopalakrishnan
ngopalak at fhcrc.org
Fri Oct 9 06:11:14 CEST 2009
Hi Aric,
I am unable to reproduce the error you get after trying out a gate that does
not have any sub populations that fall into the rectangular gate using the
GvHD dataset.
I can look into the issue if you are able to submit a reproducible example.
Nishant
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Aric Gregson
Sent: Wednesday, October 07, 2009 5:01 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Help Understand flowViz Error
Hello,
I would like to figure out why attempting to apply a gate is failing
with the error:
Error adding item 'action':
length of 'dimnames' [2] not equal to array extent
I have created a flowSet 'fs':
A flowSet with 60 experiments.
An object of class "AnnotatedDataFrame"
rowNames: TregPanel_376.fcs, TregPanel_396.fcs, ...,
TregPanel_328.fcs (60 total)
varLabels and varMetadata description:
name: name
Filename: Filename
...: ...
Infection: NA
(10 total)
column names:
FSC.A FSC.H FSC.W SSC.A SSC.H SSC.W FITC.A PE.A PE.Texas.Red.A
PerCP.Cy5.5.A PE.Cy7.A Pacific.Blue.A AmCyan.A Qdot.605.A Qdot.655.A
Indo.1..Violet..A AlexaFluor.647.A Alexa.Fluor.700.A APC.H7.A Time
And am attempting to apply this (and other similar gates) to the flowSet:
ccr7filter
Rectangular gate 'CCR7' with dimensions:
PE.Cy7.A: (5.6,Inf)
There are some tubes within the flowSet that do not have any cells
within the sub-population to which I am attempting to apply this gate
(Treg). Application of this (and the other gates) to the lymphocyte
population works without the error. I seem to remember having trouble
at some point in the past attempting to apply gates like this to a
flowSet when some tubes did not have enough of the sub-population to
apply the gate to, but it had been fixed (or so I thought?). Is it
possible that this is causing the seen error?
The flowSets were read in with ncdf and combined using the rbind2 function.
sessionInfo()
R version 2.9.2 (2009-08-24)
i386-pc-solaris2.11
locale:
C
attached base packages:
[1] grid splines stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ncdf_1.6 flowViz_1.9.8 flowCore_1.11.17
[4] rrcov_0.5-02 pcaPP_1.71 mvtnorm_0.9-7
[7] robustbase_0.4-5 Hmisc_3.7-0 survival_2.35-4
[10] colorspace_1.0-1 geneplotter_1.22.0 lattice_0.17-25
[13] annotate_1.22.0 AnnotationDbi_1.6.1 Biobase_2.4.1
[16] fortunes_1.3-6
loaded via a namespace (and not attached):
[1] DBI_0.2-4 KernSmooth_2.23-2 MASS_7.2-48
RColorBrewer_1.0-2
[5] RSQLite_0.7-2 cluster_1.12.0 feature_1.2.4 graph_1.22.2
[9] ks_1.6.6 latticeExtra_0.6-1 stats4_2.9.2 tools_2.9.2
[13] xtable_1.5-5
Thanks in advance, Aric
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