Question

flowClean error argument is of length zero

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Entering edit mode

simeen.malik • 0

@simeenmalik-14102

Last seen 7.1 years ago

Code Run:

> clean(ncfs[[11]],vectMarkers=c(7:20),filePrefixWithDir="sample_out", ext="fcs", diagnostic=TRUE)

Error in if (((vectr[id + 1] - x) == 1) & ((vectr[id + 1] - vectr[id - :
argument is of length zero

> ncfs[[11]]
flowFrame object 'ba7717f9-6eb8-4b83-801a-2988cffca804'
with 600838 cells and 21 observables:
name desc range minRange maxRange
$P1 FSC-A <NA> 262144 0.00 262143
$P2 FSC-H <NA> 262144 0.00 262143
$P3 FSC-W <NA> 262144 0.00 262143
$P4 SSC-A <NA> 262144 0.00 262143
$P5 SSC-H <NA> 262144 0.00 262143
$P6 SSC-W <NA> 262144 0.00 262143
$P7 FITC-A <NA> 262144 -107.90 262143
$P8 APC-A <NA> 262144 -111.00 262143
$P9 Alexa Fluor 700-A LiveDeadDump 262144 -111.00 262143
$P10 APC-Cy7-A CD4 262144 -111.00 262143
$P11 BV421-A <NA> 262144 -80.99 262143
$P12 BV510-A <NA> 262144 -111.00 262143
$P13 BV605-A <NA> 262144 -111.00 262143
$P14 BV650-A <NA> 262144 -111.00 262143
$P15 PE-A <NA> 262144 -99.45 262143
$P16 PE-Texas Red-A <NA> 262144 -111.00 262143
$P17 PE-Cy7-A <NA> 262144 -97.75 262143
$P18 BUV395-A <NA> 262144 -111.00 262143
$P19 BUV495-A <NA> 262144 -111.00 262143
$P20 BUV737-A CD8 262144 -111.00 262143
$P21 Time <NA> 262144 0.00 262143
305 keywords are stored in the 'description' slot

I am able to run this code on other flowFrame Objects without issues. However, some of my samples throw out this error:

Error in if (((vectr[id + 1] - x) == 1) & ((vectr[id + 1] - vectr[id - :
argument is of length zero

Any help would be appreciated!

Thanks!

flowClean • 1.4k views

ADD COMMENT • link 7.1 years ago simeen.malik • 0

score 0 · Answer 1 · 2017-10-04

Hi Simeen, Can you post your sessionInfo()? On Wed, Oct 4, 2017 at 3:34 AM, simeen.malik [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User simeen.malik <https: support.bioconductor.org="" u="" 14102=""/> wrote Question: > flowClean error argument is of length zero > <https: support.bioconductor.org="" p="" 101129=""/>: > > Code Run: > > > clean(ncfs[[11]],vectMarkers=c(7:20),filePrefixWithDir="sample_out", > ext="fcs", diagnostic=TRUE) > > Error in if (((vectr[id + 1] - x) == 1) & ((vectr[id + 1] - vectr[id - : > argument is of length zero > > > ncfs[[11]] > flowFrame object 'ba7717f9-6eb8-4b83-801a-2988cffca804' > with 600838 cells and 21 observables: > name desc range minRange maxRange > $P1 FSC-A <na> 262144 0.00 262143 > $P2 FSC-H <na> 262144 0.00 262143 > $P3 FSC-W <na> 262144 0.00 262143 > $P4 SSC-A <na> 262144 0.00 262143 > $P5 SSC-H <na> 262144 0.00 262143 > $P6 SSC-W <na> 262144 0.00 262143 > $P7 FITC-A HELIOS 262144 -107.90 262143 > $P8 APC-A TIGIT 262144 -111.00 262143 > $P9 Alexa Fluor 700-A LiveDeadDump 262144 -111.00 262143 > $P10 APC-Cy7-A CD4 262144 -111.00 262143 > $P11 BV421-A CD39 262144 -80.99 262143 > $P12 BV510-A CD15s 262144 -111.00 262143 > $P13 BV605-A CD25 262144 -111.00 262143 > $P14 BV650-A Ki67 262144 -111.00 262143 > $P15 PE-A PI16 262144 -99.45 262143 > $P16 PE-Texas Red-A Foxp3 262144 -111.00 262143 > $P17 PE-Cy7-A PD1 262144 -97.75 262143 > $P18 BUV395-A CD45RA 262144 -111.00 262143 > $P19 BUV495-A CD3 262144 -111.00 262143 > $P20 BUV737-A CD8 262144 -111.00 262143 > $P21 Time <na> 262144 0.00 262143 > 305 keywords are stored in the 'description' slot > > > > I am able to run this code on other flowFrame Objects without issues. > However, some of my samples throw out this error: > > Error in if (((vectr[id + 1] - x) == 1) & ((vectr[id + 1] - vectr[id - : > argument is of length zero > > Any help would be appreciated! > > Thanks! > > ------------------------------ > > Post tags: flowClean > > You may reply via email or visit https://support.bioconductor. > org/p/101129/ >

score 0 · Answer 2 · 2017-10-04

Hi-

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6

locale:
[1] C

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

other attached packages:
[1] plyr_1.8.4 flowViz_1.38.0 lattice_0.20-35 SamSPECTRAL_1.28.0
[5] ggcyto_1.2.3 ggplot2_2.2.1 flowClust_3.12.2 flowStats_3.32.0
[9] cluster_2.0.6 fda_2.4.7 Matrix_1.2-11 flowMeans_1.34.0
[13] flowWorkspaceData_2.10.0 data.table_1.10.4 flowClean_1.12.0 gridExtra_2.3
[17] BiocInstaller_1.24.0 openCyto_1.12.1 flowWorkspace_3.20.5 ncdfFlow_2.20.2
[21] BH_1.65.0-1 RcppArmadillo_0.7.960.1.2 flowCore_1.40.6

loaded via a namespace (and not attached):
[1] mcmc_0.9-5 matrixStats_0.52.2 RColorBrewer_1.1-2 Rgraphviz_2.18.0 tools_3.3.3
[6] R6_2.2.2 KernSmooth_2.23-15 lazyeval_0.2.0 DBI_0.7 BiocGenerics_0.20.0
[11] colorspace_1.3-2 feature_1.2.13 mnormt_1.5-5 bit_1.1-12 compiler_3.3.3
[16] graph_1.52.0 quantreg_5.33 Biobase_2.34.0 SparseM_1.77 sfsmisc_1.1-1
[21] scales_0.5.0 DEoptimR_1.0-8 hexbin_1.27.1 mvtnorm_1.0-6 robustbase_0.92-7
[26] RBGL_1.50.0 stringr_1.2.0 digest_0.6.12 multicool_0.1-10 R.utils_2.5.0
[31] MCMCpack_1.4-0 rrcov_1.4-3 pkgconfig_2.0.1 htmltools_0.3.6 changepoint_2.2.2
[36] htmlwidgets_0.9 rlang_0.1.2 FNN_1.1 shiny_1.0.5 bindr_0.1
[41] zoo_1.8-0 jsonlite_1.5 gtools_3.5.0 dplyr_0.7.4 R.oo_1.21.0
[46] magrittr_1.5 Rcpp_0.12.13 munsell_0.4.3 R.methodsS3_1.7.1 stringi_1.1.5
[51] MASS_7.3-47 zlibbioc_1.20.0 grid_3.3.3 misc3d_0.8-4 knitr_1.17
[56] tcltk_3.3.3 corpcor_1.6.9 codetools_0.2-15 stats4_3.3.3 XML_3.98-1.9
[61] glue_1.1.1 latticeExtra_0.6-28 httpuv_1.3.5 MatrixModels_0.4-1 gtable_0.2.0
[66] clue_0.3-54 assertthat_0.2.0 ks_1.10.7 mime_0.5 xtable_1.8-2
[71] coda_0.19-1 IDPmisc_1.1.17 pcaPP_1.9-72 tibble_1.3.4 bindrcpp_0.2
[76] rgl_0.98.1