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Dennis.Burian@faa.gov
▴
90
@dennisburianfaagov-2126
Last seen 7.5 years ago
>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