[BioC] question with reading bead summary data into beadarray

[Ou, Jianhong]

Hi Mark,

Thanks a lot. I got it.

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On May 3, 2012, at 6:33 AM, Mark Dunning wrote:

> Hi,
> 
> It looks like there is a typo in your command. The qc.columns argument
> should be;
> 
> qc.columns=list(exprs="AVG_Signal",Detection="Detection Pval")
> 
> and you had mis-typed Dectection as Dectection. Sorry the error
> message wasn't more informative in diagnosing the problem. The names
> of the qc columns have to match the names in the ExpressionSet object
> so that the control probes can get appended correctly to the main
> expression matrix.
> 
> Regards,
> 
> Mark
> 
> 
> On Tue, May 1, 2012 at 5:36 PM, Ou, Jianhong <Jianhong.Ou at umassmed.edu> wrote:
>> Hi Mark,
>> 
>> I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code:
>> 
>>> library("beadarray")
>> Loading required package: Biobase
>> Loading required package: BiocGenerics
>> 
>> Attaching package: ‘BiocGenerics’
>> 
>> The following object(s) are masked from ‘package:stats’:
>> 
>>    xtabs
>> 
>> The following object(s) are masked from ‘package:base’:
>> 
>>    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,
>>    pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique
>> 
>> Welcome to Bioconductor
>> 
>>    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
>>    and for packages 'citation("pkgname")'.
>> 
>> Loading required package: ggplot2
>> Welcome to beadarray version 2.6.0
>> beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
>>> setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput")
>>> dataFile = "AsuragenMAQC-probe-raw.txt"
>>> qcFile = "AsuragenMAQC-controls.txt"
>>> BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID",skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detection Pval"))
>> Error in QC[[index]] = data[[i]] :
>>  attempt to select less than one element
>> In addition: Warning message:
>> In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,  :
>>  controlIDs non-unique: 6 repeated entries have been removed.
>> 
>> and
>>> sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] beadarray_2.6.0    ggplot2_0.9.0      Biobase_2.16.0     BiocGenerics_0.2.0
>> 
>> loaded via a namespace (and not attached):
>>  [1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0  colorspace_1.1-1     DBI_0.2-5            dichromat_1.2-4      digest_0.5.2
>>  [7] grid_2.15.0          IRanges_1.14.2       limma_3.12.0         MASS_7.3-18          memoise_0.1          munsell_0.3
>> [13] plyr_1.7.1           proto_0.3-9.2        RColorBrewer_1.0-5   reshape2_1.2.1       RSQLite_0.11.1       scales_0.2.0
>> [19] stats4_2.15.0        stringr_0.6
>> 
>> Could you help me to figure out this problem? Thanks.
>> 
>> Yours sincerely,
>> 
>> Jianhong Ou
>> 
>> jianhong.ou at umassmed.edu<mailto:jianhong.ou at umassmed.edu>
>> 
>> 
>> 
>>        [[alternative HTML version deleted]]
>> 
>> 
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