[BioC] 2x3 ANOVA

Jeff Lande land0038 at umn.edu
Thu Jul 15 19:03:55 CEST 2004

Dear Bioconductor,
I'd like to know if I'm heading in the right direction with my analysis
and to see if anyone can answer a question about contrasts.
My data set involves two types of graft implants (allograft and
isograft) and three different time points (4, 14 and 25 days) with 5
replicates at each combination.  The microarray platform is the Affy
430A array and I used the gcrma package to process my data set
(indicated below)
> mouse.gcrma
Expression Set (exprSet) with
        22690 genes
        30 samples
                 phenoData object with 2 variables and 30 cases
                Gtype: read from file
                Gday: read from file
I have set up a model with no variables
            lm.empty <- function(y) lm(y ~ 1)
            lm.e <- esApply(mouse.gcrma,1,lm.empty)
, a model with only time point effect 
            lm.day <- function(y) lm(y~Gday)
            lm.d <- esApply(mouse.gcrma,1,lm.day)
and a full model
            lm.full <- function(y) lm(y~Gtype*Gday)
lm.f <- esApply(mouse.gcrma,1,lm.full).
I have used the anova function to get p-values for differences between
empty/full and day/full and then used multtest to account for multiple
Now, I'd like to start running some contrasts to see the effects at
particular graft type/day combinations (ie 14 day allografts) and also
look at fold changes.  I think both of these functions are possible
within the factDesign package, but I'm not sure how to input the second
and the third parameters in the par2lambda function.  If there's anyone
who can give me some direction on this, I would greatly appreciate it.
Jeff Lande
Graduate Student - University of Minnesota 

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