Entering edit mode
Steve Taylor
▴
280
@steve-taylor-2838
Last seen 10.3 years ago
Hi,
I am trying to run the following command in the cellHTS2 package
out<-writeReport(cellHTSlist=list(raw=x,normalized=xn,scored=xsc),forc
e=TRUE,plotPlateArgs=TRUE,imageScreenArgs=list(zrange=c(-4,8),ar=1),ma
p=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
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Medical Sciences Division
Weatherall Institute of Molecular Medicine
Oxford University