[BioC] in-group missing arrayQualityMetrics()

Fri Feb 7 21:58:39 CET 2014

Dear Wolfgang,

I have figured out a workaround
My dat seems to be a GeneFeatureSet object:

> dat
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 48 samples
  element names: exprs
protocolData
  rowNames: 01_4T1_mouse1.CEL 02_4T1_mouse2.CEL ... 48_R3T_mouse4.CEL
    (48 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: 01_4T1_mouse1.CEL 02_4T1_mouse2.CEL ... 48_R3T_mouse4.CEL
    (48 total)
  varLabels: ChipType SampleID ... DatePrepared (13 total)
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.mogene.1.0.st.v1

I think the arrayQualityMetrics() function takes in objects such as
ExpressionSet and NChannelSet, etcŠ.

So I used the Biobase package to convert to an ExpressionSet like below:

>raw.expr=exprs(dat)

>minimalSet <- ExpressionSet(assayData=raw.exprs)

This seems to work now.

I do have another question. I have a factor (grouping) that has 12 levels.
However only the first 9 are used. Is there a way to set the maximum to a
number higher than 9. For example this is the error and warning messages I
receive. Also, if you can explain what the error message means and how to
fix it that would be helpful.

The directory 'QC_Normalized_SampleID' has been created.
Error in UseMethod("xmlAttrs", node) :
  no applicable method for 'xmlAttrs' applied to an object of class "NULL"
In addition: Warning messages:
1: In maximumLevels(fac, n = length(colors)) :
  A factor was provided with 12 levels, but only the first 9 were used for
coloring.
2: In maximumLevels(fac, n = length(colors)) :
  A factor was provided with 12 levels, but only the first 9 were used for
coloring.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Thank you so much!

On 2/6/14 6:27PM, "Wolfgang Huber" <whuber at embl.de> wrote:

>Dear Guest
>
>Thank you for the report. The vignette of the package contains examples
>where the Œintgroup¹ 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 Œdat¹, 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
>>> 
>> 
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
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