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Darlene Goldstein
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230

@darlene-goldstein-1004
Last seen 7.2 years ago

hi.......
Richard Friedman <friedman at="" ...=""> writes:
>
> Dear Bioconductor Users,
> I am trying to use LimmaGUI to analyze a CpG island experiment.
>
> I wish to calculate the statistical significance associated with the
> comparison
> (Tumor Undigested-Tumor Digested) vs. (Normal Undigested-Normal
> digested).
> (Undigested has both methylated and unmethylated CpG islands.
Digested
> has only
> Unmethylated CpG islands. So Undigested-Digested gives the extent of
> methylation.
>
> Comparing tumor to normal gives the change in methylation associated
> with cancer.
>
>
>
> Mytarget matrix is:
> SlideNumber FileName Cy3 Cy5 Date
>
> 18370n_13430283.spot Ndigest Nundigest 10/3/06
> 28370n_13430572.spot Nundigest Ndigest 10/3/06
> 38370t_13469544.spot Tdigest Tundigest10/17/06
> 48370t_13469546.spot TundigestTdigest 10/17/06
>
>
<snip>
You are trying to estimate an interaction (ie, 'difference of
differences'). The
message explains why it is not possible to do this with the present
design:
the design is unconnected. The present design looks like:
ND ---> NU
ND <--- NU
TD ---> TU
TD <--- TU
so there is no path connecting any N with any T. To estimate the
interaction
you will also need hybs like Nx ---> Ty (and/or vice versa), where x
and y are D
and/or U. Then you can use limma/limmaGUI to estimate the difference
you are
interested in.
Best regards,
Darlene
--
Darlene Goldstein
?cole Polytechnique F?d?rale de Lausanne (EPFL)
Institut de math?matiques
B?timent MA, Station 8 Tel: +41 21 693 5565
CH-1015 Lausanne Fax: +41 21 693 4303
SWITZERLAND