Dear BioC,

I want to make an multivariate analysis on a multiple condition
experimental design, in which I have one reference control. The profile
is performed on 2 independent gene expression technologies Exp1 and
Exp2. In Exp2 I have only 1 interrogation for the controls,
and duplicate for all the others. I want to find differentially
regulated genes and cross validate the results from the two
technologies.

I was considering SAM (Multivariate Analysis) and Limma packages as
options, but I got problems in Exp2.

In SAM with multivariate analysis I had to remove the simplicate, in
order to make it run, (I think because it could not calculate variance
in the anova formula). But in this way the analysis is not reproducible
with Exp1 one in which the controls are considered, isn't?

on the other side, with Limma I retrive poor results.

What would you suggest? Is there a way to introduce the simplicate point
in the Sam Multivariate analyis? as it is performing Anova it could add
information in the calculation of the delta between the Groups. Do you think
it is fair to remove the experiment in the SAM Analysis, or it wold be
definitelly more appropriate Limma.

Treat Exp2 as a paired experiment?

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