[BioC] chip removal from lumiBatch object

James W. MacDonald jmacdon at uw.edu
Fri Aug 1 16:42:01 CEST 2014

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.



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.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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