[BioC] cluster genes based on expression pattern

[Moshe Olshansky]

Hi Stijn,

Thank you for your note.
Are you doing Pearson correlation on the data itself or it's logarithm?
What is the title of the book you mentioned?

Best regards,
Moshe.

>
> On Fri, Jun 17, 2011 at 10:49:08AM +1000, Moshe Olshansky wrote:
>> Hi Rabe,
>>
>> You can check timecourse package (Bioconductor).
>> Sean's suggestion to filter genes is always a good idea.
>> My naive approach would be to define a sensible distance between two
>> genes
>> and use this distance for clustering (one possibility is hclust).
>> To define a distance, suppose that you have two genes, A and B and n+1
>> time points: 0,1,...,n. Let Ai and Bi be expression levels of genes A
>> and
>> B at time i (i=0,1,...,n). One possibility is just the Lp distance (for
>> a
>> suitable p). Another possibility is to say that we do not care about the
>> absolute abundance but only about how it evolves in time and then we can
>> look at AAi = Ai/A1 and BBi = Bi/B1, i=1,2,...,n and take some Lp (or
>> other) distance between AA and BB.
>> These are just some suggestions. You may think of another reasonable
>> distance.
>
>
> Another good choice is Pearson correlation or the absolute value
> of Pearson correlation (in that case, anti-correlated genes
> will cluster with correlated genes).
>
> In our lab we have had good experiences with a network-based approach.
> In this case one chooses a certain threshold, and only retains node-pairs
> for which the (absolute) Pearson correlation falls above that threshold.
> It is possible/advisable to vary such a threshold and look at graph
> statistics such as average node degree and number of singletons to
> get an idea for an appropriate threshold.
>
> From there on, any graph clustering can be used. We use MCL (developed
> in our lab, so naturally). With MCL it pays to further transform the data,
> but I will not elaborate here. Cei Abreu-Goodger and I have written
> a book chapter on this subject, available for anyone interested.
>
> regards,
> Stijn
>
>
> --
> Stijn van Dongen         >8<        -o)   O<  forename pronunciation:
> [Stan]
> EMBL-EBI                            /\\   Tel: +44-(0)1223-492675
> Hinxton, Cambridge, CB10 1SD, UK   _\_/   http://micans.org/stijn
>



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