[BioC] Linear models with different platforms

[fhong@salk.edu]

If you are interested in finding DE (differetially expressed ) genes, you
can try RankProd, which combines data from different platforms without
assuming equal variance. For linear model without assuming equal variance,
it sounds to me that you shouldn't use one linear model since you won't
gain  any d.f. in estimating error variance.

Fangxin



> I have a pretty interesting dataset that involves three phenotypes
> (tumor/normal/cell line) on two different array platforms (quite
> different).
> I am interested in fitting a linear model but I do not want to assume that
> the variance on the two different platforms is the same (it is clearly
> not).
> The samples are all biological replicates.  Any suggestions?
>
> Thanks,
> Sean
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>


--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105