[BioC] Help Understand flowViz Error

[Nishant Gopalakrishnan]

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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