[BioC] Handling "nested" factors in limma
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Mon Dec 6 14:41:35 CET 2004
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
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