ERROR: filter,flowSet,filter fails: trying to generate an object from a virtual class ("tmixFilterResultList")

[malcook]

I find that the flowCore glue fails where flowClust succeeds.

The following, using your example data, demonstrates the issue

fcsFile <- system.file("extdata", "0877408774.B08", package="flowCore")                                                                                                                                                                      
samp <-  read.FCS(fcsFile, transformation="linearize")                                                                                                                                                                                       
fc<-flowClust(samp,varNames=c( "FSC-H","SSC-H"), K=1:3, B=100)                                                                                                                                                                               
plot(fc,data=samp)
 # the above shows three clusters.  So far so good!                                                                                                                                                                                                   

# But, the following fails
s2filter <- tmixFilter("s2filter", c( "FSC-H","SSC-H"), K=1:3, B=100)                                                                                                                                                                        
res2f <- filter(samp, s2filter)                                                                                                                                                                                                              
The prior specification has no effect when usePrior=no                                                                                                                                                                                       
Using the parallel (multicore) version of flowClust with 4 cores                                                                                                                                                                             
Error in new("tmixFilterResultList", from, subSet = factor(Map(from[[from@index]],  :                                                                                                                                                        
 trying to generate an object from a virtual class ("tmixFilterResultList")    

All done with librarys from github

library(devtools)                                                                                                                                                                                                                            
install_github('RGLab/flowCore')                                                                                                                                                                                                             
install_github('RGLab/flowViz')                                                                                                                                                                                                              
install_github('RGLab/flowStats')                                                                                                                                                                                                            
install_github('RGLab/flowClust')                                                                                                                                                                                                            
install_github('RGLab/ggcyto')   

with

sessionInfo()                                                                                                                                                                                                                             
 R version 3.2.0 (2015-04-16)                                                                                                                                                                                                                
 Platform: x86_64-unknown-linux-gnu (64-bit)                                                                                                                                                                                                 
 Running under: CentOS release 6.6 (Final)                                                                                                                                                                                                   

 locale:                                                                                                                                                                                                                                     
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C  \
              LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C                                                                                                                                                      

 attached base packages:                                                                                                                                                                                                                     
  [1] grid      splines   parallel  stats     graphics  grDevices utils     datasets  methods   base                                                                                                                                         

 other attached packages:                                                                                                                                                                                                                    
  [1] hexbin_1.27.0           ggcyto_1.5              flowStats_3.27.0        flowWorkspace_3.15.15   gridExtra_2.0.0         ncdfFlow_2.15.3         BH_1.58.0-1             RcppArmadillo_0.5.300.4 cluster_2.0.1           mvoutlier_2.0.\
 6         sgeostat_1.0-25         fda_2.4.4               Matrix_1.2-1            flowClust_3.7.01        clue_0.3-50             corpcor_1.6.8           mnormt_1.5-3            flowViz_1.33.2          lattice_0.20-31         flowCore_\
 1.35.9         ellipse_0.3-8           RBGL_1.44.0             graph_1.46.0            Biobase_2.28.0                                                                                                                                       
 [25] BiocGenerics_0.14.0     data.table_1.9.4        scales_0.2.5            ggplot2_1.0.1           devtools_1.8.0                                                                                                                         

 loaded via a namespace (and not attached):                                                                                                                                                                                                  
  [1] httr_0.6.1            assertthat_0.1        stats4_3.2.0          latticeExtra_0.6-26   robustbase_0.92-5     chron_2.3-47          digest_0.6.8          RColorBrewer_1.1-2    colorspace_1.2-6      plyr_1.8.3            pcaPP_1.9-\
 60          XML_3.98-1.3          misc3d_0.8-4          zlibbioc_1.14.0       mvtnorm_1.0-3         git2r_0.10.1          proto_0.3-10          magrittr_1.5          IDPmisc_1.1.17        memoise_0.2.1         ks_1.9.4              GGa\
 lly_0.5.0          MASS_7.3-40           xml2_0.1.1            tools_3.2.0           stringr_1.0.0         MCMCpack_1.3-3                                                                                                                   
 [28] munsell_0.4.2         rversions_1.0.1       compiler_3.2.0        pls_2.4-3             RCurl_1.95-4.6        labeling_0.3          bitops_1.0-6          gtable_0.1.2          DBI_0.3.1             reshape_0.8.5         curl_0.8  \
             reshape2_1.4.1        rrcov_1.3-8           R6_2.1.0              robCompositions_1.9.1 knitr_1.10.5          dplyr_0.4.2           sROC_0.1-2            KernSmooth_2.23-14    Rgraphviz_2.12.0      stringi_0.5-5         Rcp\
 p_0.12.0           rgl_0.95.1247         DEoptimR_1.0-3        coda_0.17-1        

[SamGG]

While I can not answer about the filter function, I think that filtering is usually done using %in%. Have you try the following command? It works nicely. But Mike will provide you a better answer.

> res2f <- samp %in% s2filter
The prior specification has no effect when usePrior=no
Using the parallel (multicore) version of flowClust with 2 cores
> res2f
Object of class 'flowClustList' 
This object consists of a list of 'flowClust' elements, each of which has the following slots:
expName, varNames, K, w, mu, sigma, lambda, nu, z, u, label, uncertainty, ruleOutliers, flagOutliers, rm.min, rm.max, logLike, BIC, ICL, prior
> plot(res2f, data=samp)
Rule of identifying outliers: 90% quantile

[mikejiang]

There is a unresolved design problem of tmixFilterResultList class.

here shows that flowCore::filter method invokes %in% method before trying to coerce the result to filterResult

When K is of length 1, %in% method returns a tmixFilterResult, which corresponds to multipleFilterResultand thus compatible with filterResult.

However, when K has length >1, %in% method returns a tmixFilterResultList, which is simply a list of tmixFilterResult and there is no equivalent class existing in flowCore. Thus the coerce method defined here is problematic.

The workaround will be looping through different K value and calling flowClust inside of the loop. e.g.

res2f <- lapply(1:3, function(k){
s2filter <- tmixFilter("s2filter", c( "FSC-H","SSC-H"), K=k, B=100)                                                                                                                                                                        
 filter(samp, s2filter)   })