[BioC] FlowCore: problem with reading and writing fcs files

[Maria Chikina [guest]]

I would like to save transformed FCS files however I run into the problem that when the transformed files are written and read back the parameters at data fields are of type INTEGER (even though before they were DOUBLE and they still have the correct values). This completely confuses other flow functions (for example density plotting). I can easily fix the file after reading but I would like to transform a lot of files and have them be usable by others without any qualifications. 

See example bellow:

> tmp=read.FCS("001.fcs")
Warning message:
In readBin(con = con, what = dattype, n = count, size = size, signed = signed,  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
> typeof(tmp at parameters@data[,5])
[1] "double"
> tf=transformList(colnames(tmp), logicleTransform())
> tmp1=transform(tmp,tf)
> typeof(tmp1 at parameters@data[,5])
[1] "double"
> write.FCS(tmp1, file="tmp.FCS")
[1] "tmp.FCS"
> tmp2=read.FCS("tmp.FCS")
Warning message:
In readBin(con = con, what = dattype, n = count, size = size, signed = signed,  :
  'signed = FALSE' is only valid for integers of sizes 1 and 2
> typeof(tmp2 at parameters@data[,5])
[1] "integer"




 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

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   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] gplots_2.11.3       caTools_1.14        gdata_2.13.2        gtools_3.0.0        ks_1.8.13           misc3d_0.8-4        rgl_0.93.996       
 [8] KernSmooth_2.23-10  MASS_7.3-28         ncdf_1.6.6          flowStats_1.18.0    flowWorkspace_1.6.1 ncdfFlow_1.6.1      Rgraphviz_2.4.1    
[15] gridExtra_0.9.1     hexbin_1.26.3       IDPmisc_1.1.17      XML_3.98-1.1        RBGL_1.36.2         graph_1.38.3        Cairo_1.5-5        
[22] Rcpp_0.10.6         cluster_1.14.4      mvoutlier_2.0.3     sgeostat_1.0-25     fda_2.4.0           Matrix_1.0-14       flowViz_1.24.0     
[29] lattice_0.20-23     flowCore_1.26.3     rrcov_1.3-4         pcaPP_1.9-49        mvtnorm_0.9-9996    robustbase_0.9-10   Biobase_2.20.1     
[36] BiocGenerics_0.6.0 

loaded via a namespace (and not attached):
 [1] bitops_1.0-6          car_2.0-19            compositions_1.30-2   energy_1.6.0          feature_1.2.10        latticeExtra_0.6-26   nnet_7.3-7           
 [8] pls_2.4-3             RColorBrewer_1.0-5    robCompositions_1.6.4 stats4_3.0.2          tensorA_0.36         

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