[BioC] Help Handling potential siRNA off target effects

[Wolfgang Huber]

Bryony

from what I understand from your mail, your question has nothing to do 
with off-target effects. And the first thing you should do at this point 
is talk to the person who designed and performed the experiment.

	Best wishes
	Wolfgang

On 28/09/10 23:52, Lloyd, Bryony wrote:
> Hi,
>
> I was hoping that someone might be able to suggest a way forward with some siRNA array data I have been asked to analyse. There are 3 cell lines, each hybridised using triplicate samples onto Agilent two colour arrays:
>
> CL, CL_knockdown and CL_scrambled.
>
> Only one siRNA that has been used against the target.
> I have analysed the data with Limma, using CL_scrambled as the ref in the design matrix. Unfortunately there are a substantial number of differentially expressed genes between the CL and CL_scrambled which will potentially confound the experiment.
> Is there a recommended way to minimise the effect of potential off target effects, is this a possibility?
>
> Possibly contrasting (CL_knockdown) - ( CL) ?
> Remove the intersection of differentially expressed genes between CLvs CL_scrambled  and CL-knockdown vs CL_scrambled ?
>
>
> I'd appreciate any advice that you can give.
>
> Bryony
>
>
>
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>
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-- 


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