read.FCS error on FCS import
1
0
Entering edit mode
@kipper-fletez-brant-6421
Last seen 6.1 years ago
United States

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

 

 

 

 
flowcore • 1.4k views
ADD COMMENT
1
Entering edit mode

It is a bug. I've pushed the fix to flowCore 1.36.1.

ADD REPLY
0
Entering edit mode
@kipper-fletez-brant-6421
Last seen 6.1 years ago
United States

Thanks Mike, this works now!

ADD COMMENT

Login before adding your answer.

Traffic: 619 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6