When I last worked with LumiBatch objects, I found that the [, -9] method
did not subset control probes data.  I'm pasting a work-around I used -
apologies to maintainers that I didn't think at the time to report this.

lumi.subset <- function(lumibatch.obj,index){

##--------------------------------------------------------------------------

##--------------------------------------------------------------------------
  ## a work-around for a shortcoming in the lumibatch object, which does
  ## not subset control data when subsetting the object.

##--------------------------------------------------------------------------
  ##lumibatch.obj: a lumibatch object to be subsetted
  ##index: an integer or logical vector specifying which samples to extract
  ##       from the lumibatch object

##--------------------------------------------------------------------------

##--------------------------------------------------------------------------
  if(!(class(index)=="integer" | class(index)=="logical")){
    error("index must be of type integer or logical")
  }
  ##temporarily set warn=-1 to suppress the warning you get when
  ##indexing a lumibatch object, since this function is a workaround
  ##to that limitation.
  options(warn=-1)
  lumibatch.reduced <- lumibatch.obj[,index]
  options(warn=0)
  controls.all <- getControlData(lumibatch.obj)
  controls <-
controls.all[,c(match(c("controlType","ProbeID",sampleNames(lumibatch.reduced)),colnames(controls.all)))]
  if(all.equal(sampleNames(lumibatch.reduced),colnames(controls)[-1:-2])){
    lumibatch.reduced <- addControlData2lumi(controls,lumibatch.reduced)
    print("Control data was correctly subsetted and inserted into the new
lumibatch object.")
  }else{
    error("couldn't match control data with reduced lumibatch object")
  }
  return(lumibatch.reduced)
}



On Fri, Aug 1, 2014 at 10:42 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Anastasia,
>
> LumiBatch objects are direct extensions of the ExpressionSet class, so can
> be subsetted using the '[' operator:
>
> > smallLumi <- lumiBarnes[,-9]
> p> pData(phenoData(smallLumi))
>              sampleID label pctBlood pctPlacenta replicate
> A01            100USA   A01      100           0         A
> A02          95US:5PA   A02       95           5         A
> A03         75US:25PA   A03       75          25         A
> A04         50US:50PA   A04       50          50         A
> A05         25US:75PA   A05       25          75         A
> A06             100PA   A06        0         100         A
> A07              PBMC   A07       NA          NA         A
> A08 Illumina Control    A08       NA          NA         A
> B02          95US:5PB   B02       95           5         B
> B03         75US:25PB   B03       75          25         B
> B04         50US:50PB   B04       50          50         B
> B05         25US:75PB   B05       25          75         B
> B06             100PB   B06        0         100         B
> B07           PaxGene   B07       NA          NA         B
> B08  Illumina Control   B08       NA          NA         B
>
> So you can see I removed the B01 sample.
>
> Best,
>
> Jim
>
>
>
>
> On 7/31/2014 6:09 PM, Kilo Morkowi wrote:
>
>> Hi,
>>
>> I wil be very grateful if you could advise me on how can I correctly
>>  remove an outlier chip from llumiBatch object.
>>
>> For instance, let's assume that B01 sample in lumiBarnes example is an
>> outlier. I'd like to remove it before normalization.
>>
>> How can this be done? Is here a method for deleting a chip?
>>
>> Many thanks for your help,
>> --- Anastasia
>>
>> ps.
>> I have imported data with lumiR function, added control info, modified
>> phenoData, and made QC and plots.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
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>> Search the archives: http://news.gmane.org/gmane.
>> science.biology.informatics.conductor
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
> _______________________________________________
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> Bioconductor@r-project.org
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> science.biology.informatics.conductor
>



-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org

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