Hi all,
Apologies if this is an easy fix, but I came across an error whilst trying to use flowcore to make a transformed filter on my flow cytometry data.
The aim to is to transform the data using the logicle transformation, and gate around a set of cells using an ellipse-shaped filter
Here is my code:
**# filter out dead cells: y <- read.FCS(emptyValue = F, "Tgalcalibration28-6-1924h1.fcs", transformation=FALSE,alter.names=TRUE) tFilter = transform("FSC.A"=logicleTransform, "SSC.A"=logicleTransform) ematrix <- matrix(c(1.1, 0.3, 0.5, 0.6), ncol=2, dimnames=list(c("FSC.A", "SSC.A"), c("FSC.A", "SSC.A"))) mean <- c("FSC.A"=4.4, "SSC.A"=4.01) egate <- ellipsoidGate(cov=ematrix, mean= mean) %on% tFilter no_dead <- Subset(y, egate) %on% tFilter
It runs fine until the final line, which throws the error:
Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is not valid for @‘transformationId’ in an object of class “transform”; is(value, "character") is not TRUE
Which I can't make head or tail of.
Is the issue related to the use of the logicle transform, which the transformed gate isn't designed for.
This is the output of sessionInfo():
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x8664-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LCTIME=EnglishUnited States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flowStats3.40.1 ggcyto1.10.2 flowWorkspace3.30.2 ncdfFlow2.28.1 flowViz1.46.1 cluster2.1.0
[7] BH1.69.0-1 RcppArmadillo0.9.500.2.0 ggplot23.2.0 lattice0.20-38 flowCore1.51.7 usethis1.5.0
[13] devtools2.0.2
loaded via a namespace (and not attached):
[1] mclust5.4.4 Rcpp1.0.1 mvtnorm1.0-11 prettyunits1.0.2 ps1.3.0 assertthat0.2.1 rprojroot1.3-2 digest0.6.19
[9] plyr1.8.4 R62.4.0 backports1.1.4 stats43.6.0 pcaPP1.9-73 pillar1.4.2 zlibbioc1.28.0 rlang0.4.0
[17] lazyeval0.2.2 curl3.3 rstudioapi0.10 data.table1.12.2 callr3.2.0 Rgraphviz2.26.0 hexbin1.27.3 Matrix1.2-17
[25] splines3.6.0 desc1.2.0 stringr1.4.0 munsell0.5.0 compiler3.6.0 pkgconfig2.0.2 BiocGenerics0.30.0 pkgbuild1.0.3
[33] IDPmisc1.1.19 tidyselect0.2.5 gridExtra2.3 tibble2.1.3 matrixStats0.54.0 XML3.98-1.20 crayon1.3.4 rrcov1.4-7
[41] dplyr0.8.2 withr2.1.2 MASS7.3-51.4 grid3.6.0 gtable0.3.0 magrittr1.5 scales1.0.0 graph1.60.0
[49] KernSmooth2.23-15 stringi1.4.3 cli1.1.0 fs1.3.1 remotes2.1.0 latticeExtra0.6-28 robustbase0.93-5 RColorBrewer1.1-2
[57] tools3.6.0 Biobase2.44.0 glue1.3.1 DEoptimR1.0-8 purrr0.3.2 ks1.11.5 processx3.3.1 pkgload_1.0.2
Any help with this issue would be much appreciated
Nick