I am trying to use flowCore's read.FCS() to import data into an R session. When I do this, I get the following error:
library(flowCore)
fs <- list.files(path="~/data_temp", pattern="fcs", full.names=TRUE)
!> read.FCS(fs[[1]])
Error in .readFCSdataRaw(con, dattype, count = as.integer(offsets["dataend"] - :
object 'splitInt' not found
However, when I try do the following, I do not get this error:
> library(flowClean)
> data(synPerturbed)
> write.FCS("~/Desktop/temp.fcs")
[1] "~/Desktop/temp.fcs"
Warning message:
In write.FCS(synPerturbed, "~/Desktop/temp.fcs") :
'write.FCS' is not fully tested and should be considered as experimental.
!> read.FCS("~/Desktop/temp.fcs")
flowFrame object '9301d9e4-a160-477f-a5fb-ee7d785d5655'
with 76466 cells and 17 observables:
name desc range minRange maxRange
$P1 FSC-A <NA> 262144 0.00000 262144
$P2 FSC-H <NA> 262144 0.00000 262144
$P3 SSC-A <NA> 261589 0.00000 261589
$P4 Time <NA> 2048 0.00000 2048
$P5 <B515-A> CD27 FITC 260954 -26.88460 260954
$P6 <V705-A> CD57 QD705 261947 -111.00000 261947
$P7 <G560-A> CD95 PE 261196 -111.00000 261196
$P8 <G660-A> CD28 Cy5 PE 261507 -111.00000 261507
$P9 <G710-A> CD244 Cy55 PE 261763 -111.00000 261763
$P10 <G780-A> CD31 Cy7 PE 261402 -111.00000 261402
$P11 <R710-A> CCR7 Ax680 261602 -111.00000 261602
$P12 <R780-A> CD3 H7 APC 261301 -111.00000 261301
$P13 <V450-A> CD127 BV421 260964 -35.98385 260964
$P14 <V545-A> Aq Blu 260949 -22.20724 260949
$P15 <V585-A> CD8 QD585 261965 -111.00000 261965
$P16 <R660-A> CD45RA APC 261023 -96.50925 261023
$P17 <V605-A> CD4 BV605 261131 -111.00000 261131
212 keywords are stored in the 'description' slot
That is, this problem happens sometimes. Any troubleshooting advice would be appreciated.
!> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flowClean_1.6.0 flowCore_1.36.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 lattice_0.20-33 mvtnorm_1.0-3
[4] changepoint_2.1.1 corpcor_1.6.8 zoo_1.7-12
[7] rrcov_1.3-8 grid_3.2.2 stats4_3.2.2
[10] pcaPP_1.9-60 graph_1.48.0 robustbase_0.92-5
[13] tools_3.2.2 Biobase_2.30.0 bit_1.1-12
[16] DEoptimR_1.0-4 sfsmisc_1.0-28 parallel_3.2.2
[19] compiler_3.2.2 BiocGenerics_0.16.0 cluster_2.0.3
It is a bug. I've pushed the fix to flowCore 1.36.1.