Have you tried loading without "phenoData = (pData)" to make sure that it is not caused by pData supplied?

~Mike 


-----Original Message-----
From: Stephan Fuhrmann [mailto:stephan.fuhrmann@charite.de]
Sent: Wed 10/5/2011 3:32 AM
To: bioconductor@r-project.org
Subject: [BioC] [flowCore] problems with read.flowSet
 
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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