[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.
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.
>
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--
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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