[BioC] Bioconductor Digest, Vol 100, Issue 28

[Dennis.Burian at faa.gov]

>Hi Everyone

>I use custom designed chicken high-density multiplex one channel
microarray (NimbleGen 12x135K). My usual >pipeline includes mostly oligo,
arrayQualityMetrics, preprocessCore, genefilter, GeneSelector and limma. So
>far I only worked with simple design, 2 conditions; control/treatment
style. Now I have a dataset with >embryonic development timeline for male
and female chicks. I still compare different timepoints using limma >but I
want to do 2 way anova to identify interaction significant genes, ie genes
where gender influences >development timeline. I looked at many packages
and could not find 2 way anova, though I am sure it is there >somewhere. I
tested package ABarray that seemed ideal for my me but after days of trying
I contacted the >author to find out that expression sets (mine is coming
from limma) can no longer be used by ABarray  as the >package has not been
updated for a while.  Can anyone suggest a package (and an example code if
possible) for >2 way anova? I am so tempted to go and do it in
GeneSpring...

>Thanks all

>Dana

Dana,
The timecourse package is designed to handle temporal data across
biological conditions and we've had good results from this package.  I will
add that we've compared expression between genders in temporal data and the
most significant genes are sex-linked.

Dennis Burian, Ph.D.
FAA Functional Genomics Group
405-954-6087
dennis.burian at faa.gov