On Mon, Nov 26, 2012 at 7:50 AM, Alyaa Mahmoud <alyamahmoud@gmail.com>wrote:

> On Mon, Nov 26, 2012 at 1:51 PM, Robert Castelo <robert.castelo@upf.edu
> >wrote:
>
> > hi,
> >
> > few more questions,
> >
> > how many samples do you have?
> >
> 257
>
> >
> > what is the structure of these data: are all samples from the same
> > experimental condition?
> >
> yes
>
> >
> > do you suspect the presence of some confounding factors such as batch,
> > gender (if applicable), strain (if applicable), etc...
> >
> not really, I need to obtain sets of correlated genes (in
> expression/regulation...etc) and then re-cluster using these sets and
> observe the pattern of samples clustering.
>
> >
> > are you looking for some specific type of correlated genes, such as
> > targets of DNA or RNA binding proteins?
> >
> no, I am more interested in the behaviour of the samples rather, but I want
> to re-cluster using subsets of the genes.
>
>
Hi, Alyaa.

Have you tried creating a heatmap using the top 200 (just to pick a number)
most variable genes?  Heatmaps usually cluster both samples and genes and
does something that sounds quite similar to what you are describing that
you want to do.

Sean


> >
> >
> > robert.
> >
> >
> > On 11/26/2012 12:34 PM, Alyaa Mahmoud wrote:
> >
> >> Hi Dr Castelo
> >>
> >> Gene expression dat
> >>
> >> Thanks
> >>
> >>
> >> On Mon, Nov 26, 2012 at 1:28 PM, Robert Castelo <robert.castelo@upf.edu
> >> <mailto:robert.castelo@upf.edu**>> wrote:
> >>
> >>     hi Alyaa,
> >>
> >>     from what kind of data?
> >>
> >>     cheers,
> >>     robert.
> >>
> >>
> >>     On 11/22/2012 10:14 AM, Alyaa Mahmoud wrote:
> >>
> >>         Dear Group
> >>
> >>         What the most convenient direct way of identifying sets of
> >>         correlated genes
> >>         ?
> >>
> >>         Thanks a lot
> >>         Alyaa
> >>
> >>
> >>     --
> >>     Robert Castelo, PhD
> >>     Associate Professor
> >>     Dept. of Experimental and Health Sciences
> >>     Universitat Pompeu Fabra (UPF)
> >>     Barcelona Biomedical Research Park (PRBB)
> >>     Dr Aiguader 88
> >>     E-08003 Barcelona, Spain
> >>     telf: +34.933.160.514 <tel:%2B34.933.160.514>
> >>     fax: +34.933.160.550 <tel:%2B34.933.160.550>
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Alyaa Mahmoud
> >>
> >> "Love all, trust a few, do wrong to none"- Shakespeare
> >>
> >>
> > --
> > Robert Castelo, PhD
> > Associate Professor
> > Dept. of Experimental and Health Sciences
> > Universitat Pompeu Fabra (UPF)
> > Barcelona Biomedical Research Park (PRBB)
> > Dr Aiguader 88
> > E-08003 Barcelona, Spain
> > telf: +34.933.160.514
> > fax: +34.933.160.550
> >
>
>
>
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
>         [[alternative HTML version deleted]]
>
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