[BioC] flowStats warpSet Unpredictable Completion

[Chao-Jen Wong]

Hi, Aric,

I've never seen this type error before, but I guess the bugs occur when
the warpSet.R is trying to identify the landmarks of the density kernel
estimates of one of the stain channel.  Is it possible for you to send
me the flowSet so that I can reproduce the error and possibly fix the bugs?

Thanks,
Chao-Jen

On 06/02/10 19:46, Aric Gregson wrote:
> Hello,
>
> 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` = 
> c(10000,13000,20000,40000,60000,80000,100000,160000,200000,263000,263000, 
> 200000,160000,100000,80000,60000,40000,20000,14000,8000),
>   `FSC.H` = 
> c(5000,5000,10000,22000,34000,50000,65000,115000,150000,200000,220000,170000,130000,78000,62000,45000,30000,15000,10000,5000),
>   filterId="Singlet")
> add(wf, singletfilter, parent="boundaryfilter+")
> asinhtf <- transformList(colnames(fs)[4:19],
>                          asinh,
>                          transformationId="asinh")
> 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"),
>                       plot=FALSE,
>                       filterId="CD3CD4",
>                        positive=T)
> add(wf, qgate, parent="Warping")
> ================
> sessionInfo()
> R version 2.11.0 (2010-04-22) 
> amd64-portbld-freebsd8.0 
>
> locale:
> [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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>   


-- 
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