[BioC] Microarray experiment design issues

[David Westergaard]

Hi Ali,

I don't think this list is appropriate to answer these questions,
since it doesn't generally involve any bioconductor packages.

However, I don't really see why you would have a problem in A. Are
both cell lines not exposed to the same variation in humidty levels,
temperature, oxygen levels, etc, so that you would expect the same
variation due to these factors in both treated and untreated, and thus
the total variation due to these factors would be approximately zero?
Also, could the technically noise not potentially cause too great a
distance between arrays to pick up any variation, in setup B?
I don't really have any experience with experimental setup, so the
above comments are just my logical conclusions from working with
microarray data.

Best,
David


2012/6/15 Ali Tofigh <alix.tofigh at gmail.com>:
> Our goal is to measure the effects of a treatment on a specific cell line
> using gene expression microarrays (agilent 2-color). There are two possible
> experimental designs:
>
> A) perform the entire experiment in one day: split cells into 6 groups,
> treat 3 with compound and leave 3 untreated. This setup minimizes technical
> variation, but the list of differentially expressed genes will include some
> that are differentially expressed mainly due to the specific conditions on
> the day of the experiment (humidty levels, temperature, oxygen levels,
> etc).
>
> B) perform the experiment on three separate occasions: each day, split
> cells into two groups, treat only one with compound. An paired analyis
> would be appropriate here. This setup introduces noise (technical noise
> because of separate handling of the three pairs and noise from daily
> variation of the environmental conditions) and so we lose some statistical
> power. However, since the experiment is performed under slightly different
> environmental conditions, some of the condition-specific genes will no
> longer show up as differentially expressed and the list of genes would in
> this sense be more robust/reproducible.
>
> Does anyone have experience with both setups? I would like to know if the
> amount of variance that is introduced in setup B can be expected to be low
> enough to not lose too much power while producing a more robust set of
> differentially expressed genes.
>
> Cheers
> /Ali
>
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