[BioC] what to do with microarray outliers?

[Jenny Drnevich]

Hi Theresa,

If you have two groups that are clearly separated on a PCA plot, 
except a couple samples are not in the "correct" group but instead in 
the other group, then I'd wager my pension* that these are 
mis-labeled samples, not outliers. I've seen this happen more than 
once, and while disturbing, we usually can never figure out exactly 
what happened. In general, outliers only refer to samples that are 
different from ALL others, not just samples that cluster with another 
group instead of their own.

HTH,
Jenny

* I work for the state of Illinois, so my pension may not be worth much :(

At 11:06 PM 4/10/2011, Wei Shi wrote:
>Hi Theresa:
>
>Maybe you can try use array weights. See ?arrayWeights in limma for 
>more details.
>
>Cheers,
>Wei
>
>On Apr 10, 2011, at 9:56 PM, Theresa Brandt wrote:
>
> > Hello,
> >
> >   I would like to ask what to do if there are outlying microarrays on PCA
> > plot. Should I remove them from the further analysis or not?
> >   I have two groups of samples and these groups are clearly separated on
> > the PCA plot (first and second PC). But a few microarrays are not in the
> > "correct" group.
> >   What to do in a situation that one of the samples is much different from
> > all the others (but technically it as a good microarray)? What would you do
> > in such a situation?
> >
> > Sincerely,
> > Theresa
> >
> >       [[alternative HTML version deleted]]
> >
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