[BioC] cellHTS2 error in writeReport

[Wolfgang Huber]

Dear Steve,

thank you for the feedback! Can you please try with cellHTS2 version
2.5.1 (you are using 2.2.5); and if the error persists, make available
to us the offending objects x, xn, xsc (or gene-anonymized versions of
them if that matters).

See http://www.bioconductor.org/packages/2.3/bioc/html/cellHTS2.html

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


06/06/2008 10:08 Steve Taylor scripsit
> 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
> 
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