[BioC] PCA plots and identifying outliers

[James W. MacDonald]

Hi Guest,

On 10/5/2012 11:35 AM, Guest [guest] wrote:
> Hi,
>
> I'm using affycoretools() to generate some pca plots. I found that I have some outliers. I was wondering, how do I find out which particular sample (.CEL file) was the outlier?
>
>   I know which group it is from, but not the identity.
>
> I've plotted pca plots with just using the plot() function as well, but I still do not know how to identify the particular sample that is the outlier.
>
> Any ideas for both affycoretools() or the general plot() function will be appreciated!

See ?plotPCA, in particular the addtext argument.

plotPCA(eset, groups, groupnames, addtext = sampleNames(eset))

Best,

Jim


>
> Thanks,
>
> Guest
>
>   -- output of sessionInfo():
>
> No error, just question about how find out further details.
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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