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 -- Sent via the guest posting facility at bioconductor.org.

I pushed the fix to flowCore 1.28.21, which will appear in one day or two. Mike On 01/29/2014 03:00 AM, bioconductor-request at r-project.org wrote: > 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" >