[Bioc-devel] what to do with microarray outliers

[Wolfgang Huber]

Dear Theresa

it is difficult to advise a specific action given such a generic 
situation. Can you go back the experimenters and figure out what went wrong?

- accidentical confusion of samples in the lab
- copy paste error in Excel
- file naming mishap
- earthshattering surprising new biology
- ...

Further action would depend on that.

	Best wishes
	Wolfgang


Il Apr/10/11 1:36 PM, Theresa Brandt ha scritto:
> 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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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber