[BioC] Handling "nested" factors in limma

[michael watson (IAH-C)]

Hi

Consider the design matrix in the limma user guide, section 10.7:

FileName	Strain	Treatment
File1	WT	U
File2	WT	S
File3	Mu	U
File4	Mu	S
File5	Mu	S

Does it matter if these samples are from five different mice, or only
two (WT and Mu) where different treatments have been applied to the same
mouse at different times?  Does this nesting change how we apply the
design and contrasts matrices in limma?

Consider also another level, a simple time of "before" and after
"treatment".  We would have something like:

FileName	Strain	Treatment	Time
File1	WT	U	Before
File2	WT	U	After
File3	WT	S	Before
File4	WT	S	After
Etc
Etc

Presumably then the contract "After - Before" would show genes which
differ due to the administration of a treatment (regardless of what the
treatment is), the contrast "S - U" would show genes changing due to the
treatment, and "WT - Mu" would look for strain effects.  But "Before"
and "After" are relative to the treatment and the mouse, rather than
specific (equivalent) moments in time;  again, does this change how we
apply limma?

Thanks in advance for your help

Mick