[BioC] flowStats warpSet Unpredictable Completion

Aric Gregson a.gregson at ucla.edu
Thu Jun 3 04:46:25 CEST 2010


I'm not sure if this is a known issue, but I have been experiencing 
unpredictable results with the warpSet function in flowStats (see 
sessionInfo at end). Essentially, I have a been experimenting with warpSet 
and have it in a script that runs through the same 5 fcs files as a flowSet 
each time. About every 2 out of 3 runs I get this error with warpSet:

pars <- colnames(Data(wf[["base view"]]))[c(12,13,18,19)] 
norm <- normalization(normFun = function(x, parameters, ...)
+                       warpSet(x, parameters, ...),
+                       parameters = pars,
+                       normalizationId= "Warping4")
add(wf, norm, parent="Lymphs+")
Estimating landmarks for channel APC.H7.A ...
Registering curves for parameter Pacific.Blue.A ...
Registering curves for parameter AmCyan.A ...
Error adding item 'action':
  Error in apply(sapply(regions[!nar], function(r) if (is.null(dim(r))) r 
else r[n, : dim(X) must have a positive length

I'm not clear why it would work sometimes and not work other times. Can 
anyone point me in the right direction to debug this a bit?

Thanks, Aric
The full short script up until this section follows:

wf <- workFlow(fs, name="2009_03_05 Asinh Workflow")
boundaryfilter <- boundaryFilter(filterId = "boundaryfilter",
                                 x = c("FSC.A", "SSC.A"))
add(wf, boundaryfilter)
singletfilter = polygonGate(`FSC.A` = 
  `FSC.H` = 
add(wf, singletfilter, parent="boundaryfilter+")
asinhtf <- transformList(colnames(fs)[4:19],
add(wf, asinhtf, parent="Singlet+")
lymphfilter <- lymphGate(Data(wf[["asinh"]]), channels=c("FSC.A", "SSC.A"), 
preselection="APC.H7.A", filterId="Lymphs", eval=FALSE, scale=2)
add(wf, lymphfilter$n2gate, parent="asinh")
pars <- colnames(Data(wf[["base view"]]))[c(10,11,12,13,18,19)] # problem 
with 18
norm <- normalization(normFun = function(x, parameters, ...)
                      warpSet(x, parameters, ...),
                      parameters = pars,
                      normalizationId= "Warping")
add(wf, norm, parent="Lymphs+")
qgate <- quadrantGate(Data(wf[["Warping"]]),
                      stains=c("AmCyan.A", "APC.H7.A"),
add(wf, qgate, parent="Warping")
R version 2.11.0 (2010-04-22) 

[1] C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] flowStats_1.6.0     cluster_1.12.3      fda_2.2.1          
 [4] zoo_1.6-3           flowQ_1.8.0         latticeExtra_0.6-11
 [7] RColorBrewer_1.0-2  parody_1.6.0        bioDist_1.20.0     
[10] KernSmooth_2.23-3   mvoutlier_1.4       outliers_0.13-2    
[13] flowViz_1.12.0      lattice_0.18-5      flowCore_1.14.1    
[16] rrcov_1.0-00        pcaPP_1.8-1         mvtnorm_0.9-9      
[19] robustbase_0.5-0-1  Biobase_2.8.0       fortunes_1.3-7     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.10.1 DBI_0.2-5            MASS_7.3-5          
 [4] RSQLite_0.9-0        annotate_1.26.0      feature_1.2.4       
 [7] geneplotter_1.26.0   graph_1.26.0         grid_2.11.0         
[10] ks_1.6.12            stats4_2.11.0        xtable_1.5-6

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