[BioC] [flowCore] problems with read.flowSet
Stephan Fuhrmann
stephan.fuhrmann at charite.de
Wed Oct 5 12:32:32 CEST 2011
dear all,
i tried to load 17 fcs-files using the read.flowSet-command:
flowData <- read.flowSet(path = "/Users/stephan/Desktop/FCS
files/IE-Studie/R_pp65_A", phenoData = (pData), transformation = FALSE)
this returned the following error:
Error in dim(colNames) <- c(ncol(from[[frameList[[1]]]]),
length(frameList)) :
Dimensionen [Produkt 170] don´t match the length of the object [17]
i can´t work out whats going wrong. loading the example data works fine.
is there anything wrong with the fcs-files?
help is much appreciated!
stephan
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] tools splines grid stats graphics grDevices utils
datasets methods
[10] base
other attached packages:
[1] flowUtils_1.12.0 flowQ_1.12.0 latticeExtra_0.6-18
RColorBrewer_1.0-5
[5] parody_1.10.0 bioDist_1.24.1 KernSmooth_2.23-6
outliers_0.14
[9] flowMerge_2.0.3 multicore_0.1-7 foreach_1.3.2
codetools_0.2-8
[13] iterators_1.0.5 snow_0.3-7 flowMeans_1.4.0
flowFP_1.8.0
[17] flowClust_2.10.0 ellipse_0.3-5 mnormt_1.4-3
flowViz_1.16.0
[21] lattice_0.19-33 xtable_1.5-6 sfsmisc_1.0-14
cluster_1.14.0
[25] mvoutlier_1.9.3 robCompositions_1.5.0 car_2.0-11
survival_2.36-9
[29] nnet_7.3-1 compositions_1.10-1 energy_1.3-0
MASS_7.3-14
[33] boot_1.3-2 tensorA_0.36 rgl_0.92.798
fda_2.2.7
[37] zoo_1.7-4 flowCore_1.18.0 rrcov_1.3-01
pcaPP_1.9-44
[41] mvtnorm_0.9-9991 robustbase_0.7-6 Biobase_2.12.2
flowType_0.99.4
[45] Rgraphviz_1.30.1 graph_1.30.0
loaded via a namespace (and not attached):
[1] annotate_1.30.1 AnnotationDbi_1.14.1 DBI_0.2-5
feature_1.2.8
[5] geneplotter_1.30.0 ks_1.8.2 RSQLite_0.9-4
RUnit_0.4.26
[9] stats4_2.13.1 XML_3.4-3
> traceback()
5: asMethod(object)
4: as(list2env(from, new.env(hash = T, parent = emptyenv())), "flowSet")
3: asMethod(object)
2: as(flowSet, "flowSet")
1: read.flowSet(path = "/Users/stephan/Desktop/FCS files/IE-Studie/R_pp65_A",
phenoData = (pData), transformation = FALSE)
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