Entering edit mode
Aric Gregson
▴
270
@aric-gregson-3058
Last seen 10.2 years ago
Hello,
I'm not sure if this is a known issue, but I have been experiencing
unpredictable results with the warpSet function in flowStats (see
sessionInfo at end). Essentially, I have a been experimenting with
warpSet
and have it in a script that runs through the same 5 fcs files as a
flowSet
each time. About every 2 out of 3 runs I get this error with warpSet:
pars <- colnames(Data(wf[["base view"]]))[c(12,13,18,19)]
norm <- normalization(normFun = function(x, parameters, ...)
+ warpSet(x, parameters, ...),
+ parameters = pars,
+ normalizationId= "Warping4")
add(wf, norm, parent="Lymphs+")
Estimating landmarks for channel APC.H7.A ...
Registering curves for parameter Pacific.Blue.A ...
Registering curves for parameter AmCyan.A ...
Error adding item 'action':
Error in apply(sapply(regions[!nar], function(r) if
(is.null(dim(r))) r
else r[n, : dim(X) must have a positive length
I'm not clear why it would work sometimes and not work other times.
Can
anyone point me in the right direction to debug this a bit?
Thanks, Aric
==============
The full short script up until this section follows:
wf <- workFlow(fs, name="2009_03_05 Asinh Workflow")
boundaryfilter <- boundaryFilter(filterId = "boundaryfilter",
x = c("FSC.A", "SSC.A"))
add(wf, boundaryfilter)
singletfilter = polygonGate(`FSC.A` =
c(10000,13000,20000,40000,60000,80000,100000,160000,200000,263000,2630
00,
200000,160000,100000,80000,60000,40000,20000,14000,8000),
`FSC.H` =
c(5000,5000,10000,22000,34000,50000,65000,115000,150000,200000,220000,
170000,130000,78000,62000,45000,30000,15000,10000,5000),
filterId="Singlet")
add(wf, singletfilter, parent="boundaryfilter+")
asinhtf <- transformList(colnames(fs)[4:19],
asinh,
transformationId="asinh")
add(wf, asinhtf, parent="Singlet+")
lymphfilter <- lymphGate(Data(wf[["asinh"]]), channels=c("FSC.A",
"SSC.A"),
preselection="APC.H7.A", filterId="Lymphs", eval=FALSE, scale=2)
add(wf, lymphfilter$n2gate, parent="asinh")
pars <- colnames(Data(wf[["base view"]]))[c(10,11,12,13,18,19)] #
problem
with 18
norm <- normalization(normFun = function(x, parameters, ...)
warpSet(x, parameters, ...),
parameters = pars,
normalizationId= "Warping")
add(wf, norm, parent="Lymphs+")
qgate <- quadrantGate(Data(wf[["Warping"]]),
stains=c("AmCyan.A", "APC.H7.A"),
plot=FALSE,
filterId="CD3CD4",
positive=T)
add(wf, qgate, parent="Warping")
================
sessionInfo()
R version 2.11.0 (2010-04-22)
amd64-portbld-freebsd8.0
locale:
[1] C
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] flowStats_1.6.0 cluster_1.12.3 fda_2.2.1
[4] zoo_1.6-3 flowQ_1.8.0 latticeExtra_0.6-11
[7] RColorBrewer_1.0-2 parody_1.6.0 bioDist_1.20.0
[10] KernSmooth_2.23-3 mvoutlier_1.4 outliers_0.13-2
[13] flowViz_1.12.0 lattice_0.18-5 flowCore_1.14.1
[16] rrcov_1.0-00 pcaPP_1.8-1 mvtnorm_0.9-9
[19] robustbase_0.5-0-1 Biobase_2.8.0 fortunes_1.3-7
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.10.1 DBI_0.2-5 MASS_7.3-5
[4] RSQLite_0.9-0 annotate_1.26.0 feature_1.2.4
[7] geneplotter_1.26.0 graph_1.26.0 grid_2.11.0
[10] ks_1.6.12 stats4_2.11.0 xtable_1.5-6