[BioC] cellHTS2 error in writeReport

[Steve Taylor]

Hi,

I am trying to run the following command in the cellHTS2 package

out<-writeReport(cellHTSlist=list(raw=x,normalized=xn,scored=xsc),force=TRUE,plotPlateArgs=TRUE,imageScreenArgs=list(zrange=c(-4,8),ar=1),map=TRUE)

but I get:

Error in `colnames<-`(`*tmp*`, value = c("pos", "activators", "inhibitors" :
   attempt to set colnames on object with less than two dimensions


Can anyone give me a hint while this is failing?

 > x
cellHTS (storageMode: lockedEnvironment)
assayData: 288 features, 1 samples
   element names: ch1
phenoData
   sampleNames: 1
   varLabels and varMetadata description:
     replicate: Replicate number
     assay: Biological assay
   additional varMetadata: channel
featureData
   featureNames: 1, 2, ..., 288  (288 total)
   fvarLabels and fvarMetadata description:
     plate: Plate number
     well: Well ID
     controlStatus: Well annotation
experimentData: use 'experimentData(object)'
state:  configured = TRUE
         normalized = FALSE
         scored = FALSE
         annotated = FALSE
Number of plates: 3
Plate dimension: nrow = 8, ncol = 12
Number of batches:
Well annotation: sample pos neg empty
Annotation:

 > xn
cellHTS (storageMode: lockedEnvironment)
assayData: 288 features, 1 samples
   element names: ch1
phenoData
   sampleNames: 1
   varLabels and varMetadata description:
     replicate: Replicate number
     assay: Biological assay
   additional varMetadata: channel
featureData
   featureNames: 1, 2, ..., 288  (288 total)
   fvarLabels and fvarMetadata description:
     plate: Plate number
     well: Well ID
     controlStatus: Well annotation
experimentData: use 'experimentData(object)'
state:  configured = TRUE
         normalized = TRUE
         scored = FALSE
         annotated = FALSE
Number of plates: 3
Plate dimension: nrow = 8, ncol = 12
Number of batches:
Well annotation: sample pos neg empty
Annotation:
 > xsc
cellHTS (storageMode: lockedEnvironment)
assayData: 288 features, 1 samples
   element names: ch1
phenoData
   sampleNames: 1
   varLabels and varMetadata description:
     replicate: Replicate number
     assay: Biological assay
   additional varMetadata: channel
featureData
   featureNames: 1, 2, ..., 288  (288 total)
   fvarLabels and fvarMetadata description:
     plate: Plate number
     well: Well ID
     ...: ...
     GeneID: GeneID
     (5 total)
experimentData: use 'experimentData(object)'
state:  configured = TRUE
         normalized = TRUE
         scored = TRUE
         annotated = TRUE
Number of plates: 3
Plate dimension: nrow = 8, ncol = 12
Number of batches:
Well annotation: sample pos neg empty
Annotation:


 > sessionInfo()
R version 2.6.1 (2007-11-26)
sparc-sun-solaris2.9

locale:
/en_GB/C/en_GB/en_GB/en_GB/en_GB

attached base packages:
  [1] tcltk     splines   grid      tools     stats     graphics  grDevices
  [8] utils     datasets  methods   base

other attached packages:
  [1] cellHTS2_2.2.5       vsn_3.2.1            limma_2.12.0
  [4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
  [7] splots_1.4.0         genefilter_1.16.0    survival_2.34
[10] prada_1.14.0         rrcov_0.4-03         robustbase_0.2-8
[13] RColorBrewer_1.0-2   Biobase_1.16.2

loaded via a namespace (and not attached):
  [1] annotate_1.16.1     AnnotationDbi_1.0.6 DBI_0.2-4
  [4] geneplotter_1.16.0  KernSmooth_2.22-21  lattice_0.17-2
  [7] MASS_7.2-38         rcompgen_0.1-17     RSQLite_0.6-4
[10] stats4_2.6.1




Many Thanks,

Steve
------------------------------------------------------------------
Medical Sciences Division
Weatherall Institute of Molecular Medicine
Oxford University