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

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),fo rce=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor