Question: cellHTS2 error in writeReport
0
gravatar for Steve Taylor
11.4 years ago by
Steve Taylor280
Steve Taylor280 wrote:
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
cellhts2 • 699 views
ADD COMMENTlink modified 11.4 years ago by Wolfgang Huber13k • written 11.4 years ago by Steve Taylor280
Answer: cellHTS2 error in writeReport
0
gravatar for Wolfgang Huber
11.4 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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
ADD COMMENTlink written 11.4 years ago by Wolfgang Huber13k
Dear Wolfgang, > > 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 > Yes. That fixed it. Thank you! Steve
ADD REPLYlink written 11.4 years ago by Steve Taylor280
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 141 users visited in the last hour