[BioC] Cross-comparison of independent intensities from different experiments (genepix) (sorry I don\'t know how to describe the problem better)

[James W. MacDonald]

Hi Susanne,

On 2/3/2012 10:27 AM, Susanne Gerber wrote:
> Dear James,
> thank you so much for the very fast and detailed response.
> I will start answering your questions:
>
>> I assume that by 'two independent time series' you mean that these experiments were conducted at different times, perhaps in different labs, etc?
> The first experiment was performed half a year earlier but within the
> same lab and by the same experimenter.

Ugh. <shoots self>

>
>> The second problem is due to the fact that you never hybridized MU and WT samples on the same chip,
>> which has introduced another untestable and unquantifiable 'chip' effect.
> Well, this is actually the problem I am struggling with.
>
>> You could hypothetically do a single channel analysis with these data,
>> but any comparison between MU and WT would include both biological and technical variability,
>> and you won't be able to say how much of either.
>> Again, you can assume that the technical variability is small, but you won't really be able to say for sure if this assumption is true.
> I think I have to do so, since these data are the only dataset I have.
> I am not an experimenter and the lab where the data originally came
> from can not perform these new experiments (the cells are not
> available any more, project ran out last year, no money, no staff...).
> Thats what I meant by saying "it is also not possible to repeat the
> experiment and produce a direct comparison."
> Sorry for being so imprecise. :)
>
> The maanova package is great and I already used it, however I still do
> not know how to perform this single channel analysis you were talking
> about with my two-colour data.
> What would be the best way (or is there already an existing package
> for this) to treat the data and to extract the information ?

Yes, look at the limma User's Guide, starting on p. 52.

Best,

Jim
>
> Thanks again so much for your help
> Best regards,
> Susanne
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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