[BioC] in-group missing arrayQualityMetrics()

[Wolfgang Huber]

Dear Guest

Thank you for the report. The vignette of the package contains examples where the ‘intgroup’ argument is used, and the package builds (http://bioconductor.org/checkResults/release/bioc-LATEST/#A). Since the only difference to your example is the dataset ‘dat’, we would need to investigate that to understand how it could possibly create the problem you report. Would it be possible for you to send me your object and the code needed to reproduce the problem, starting from a fresh R session?

	Best wishes
	Wolfgang
 
 

On 5 Feb 2014, at 23:18, guest [guest] <guest at bioconductor.org> wrote:

> 
> Hi I'm trying to run arrayQualityMetrics and I keep getting an error message saying that the intgroup is missing. However, I am very clearly specifying the intgroup and it definitely exists in my phenodata. I'm working with mogene.1.0.st.v1 arrays. Please see my error message and a few lines of my phenodata below:
> 
> Error message:
> 
>> arrayQualityMetrics(expressionset = dat, intgroup="SampleID",outdir = "QC_test", force =TRUE, do.logtransform = TRUE);
> The directory 'QC_test' has been created.
> Error in match(x, table, nomatch = 0L) : 
>  argument "intgroup" is missing, with no default
> 
> phenodata:
> 
>> pData(dat)
>                              ChipType SampleID MouseStrain       TumorOrigin
> 01_4T1_mouse1.CEL     MoGene-1_0-st-v1    4T1_1      Balb/c       Spontaneous
> 02_4T1_mouse2.CEL     MoGene-1_0-st-v1    4T1_2      Balb/c       Spontaneous
> 03_4T1_mouse3.CEL     MoGene-1_0-st-v1    4T1_3      Balb/c       Spontaneous
> 04_4T1_mouse4.CEL     MoGene-1_0-st-v1    4T1_4      Balb/c       Spontaneous
> 05_EMT-6_mouse1.CEL   MoGene-1_0-st-v1   EMT6_1      Balb/c       Spontaneous
> 06_EMT-6_mouse2.CEL   MoGene-1_0-st-v1   EMT6_2      Balb/c       Spontaneous
> 
> 
> Any suggestions on how to fix this will be appreciated.
> 
> -- output of sessionInfo(): 
> 
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
> [1] affyPLM_1.38.0             preprocessCore_1.24.0     
> [3] gcrma_2.34.0               affy_1.40.0               
> [5] arrayQualityMetrics_3.18.0 pd.mogene.1.0.st.v1_3.8.0 
> [7] RSQLite_0.11.4             DBI_0.2-7                 
> [9] oligo_1.26.0               Biobase_2.22.0            
> [11] oligoClasses_1.24.0        BiocGenerics_0.8.0        
> 
> loaded via a namespace (and not attached):
> [1] affxparser_1.34.0    affyio_1.30.0        annotate_1.40.0     
> [4] AnnotationDbi_1.24.0 beadarray_2.12.0     BeadDataPackR_1.14.0
> [7] BiocInstaller_1.12.0 Biostrings_2.30.1    bit_1.1-11          
> [10] Cairo_1.5-5          cluster_1.14.4       codetools_0.2-8     
> [13] colorspace_1.2-4     ff_2.2-12            foreach_1.4.1       
> [16] Formula_1.1-1        genefilter_1.44.0    GenomicRanges_1.14.4
> [19] grid_3.0.2           Hmisc_3.13-0         hwriter_1.3         
> [22] IRanges_1.20.6       iterators_1.0.6      lattice_0.20-24     
> [25] latticeExtra_0.6-26  limma_3.18.7         plyr_1.8            
> [28] RColorBrewer_1.0-5   reshape2_1.2.2       setRNG_2011.11-2    
> [31] splines_3.0.2        stats4_3.0.2         stringr_0.6.2       
> [34] survival_2.37-4      SVGAnnotation_0.93-1 vsn_3.30.0          
> [37] XML_3.98-1.1         xtable_1.7-1         XVector_0.2.0       
> [40] zlibbioc_1.8.0      
>> 
> 
> 
> --
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> 
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