[BioC] WGCNA_ Eigengene and sample complications correlations

[Peter Langfelder]

On Mon, Jun 30, 2014 at 5:28 AM, amit kumar subudhi <amit4help at gmail.com> wrote:
> Hi all,
>
> I have used the WGCNA framework to generate network and identify modules.
>
> Next, I wish to relate the modules with the disease status. My samples
> include malaria parasites isolated from patients with different disease
> status.
>
> For example, I have 20 malaria parasite samples of which 7 are from
> uncomplicated malaria patients, 7 are from patients with complication 1 and
>  6 are from complication 2.
>
> Is there any procedure to see the relationship of eigenegnes with specific
> disease status? More specifically to know which modules are positively or
> negatively correlates to particular group of malaria samples?

Yes, turn your 'complication' with values uncomplicated, complication
1, complication 2 into a set of binary variables: one variable that is
1 for uncomplicated and 0 for everything else, one variable that is 1
for complication 1 and zero for everything else, and one variable that
is 1 for complication 2 and zero for everything else. You could also
create pairwise comparisons, for example a variable that is 1 for
complication 1, 0 for complication 2, and missing (NA) for
uncomplicated. Then correlate the eigengenes to the binary indicators.

Best,

Peter