Hello All:
I am Yogender Gowtham, a graduate student from Clemson University. We are
using RNA-Seq to investigate the transcriptional changes of Chinese Hamster
Ovary (CHO) cells during serum-free adaptation. Our experiment has two cell
lines, say Y and Z, under 3 different serum concentrations, say, 10%, 5%
and 0%. Cell line Z could not be adapted to 0% serum condition and hence we
have unbalanced set of conditions. For clarity, the conditions are listed
below
A - Y at 0% D - Z at 5%
B - Y at 5% E - Z at 10%
C - Y at 10%
We have come up with 9 different pairwise comparisons based on the
scientific questions we want to answer. But performing so many pairwise
comparisons will lead to more liberal FDR values. Hence we want to perform
ANOVA analysis on all the five conditions.
Based on section 3.2.6 which explains how to perform ANOVA-like analysis.
>From what I understand, it contrasts each column with intercept and will
list any differences that are non-zero (B-A, C-A, D-A, E-A). But ideally we
want B-A, B-C, B-D, E-B, C-A, D-C, E-C, D-A, or E-A comparisons in an ANOVA
test.
If anyone can suggest a method on edgeR to perform ANOVA tests, that will
be perfect. If not, can someone suggest other possible packages that could
help me do an ANOVA analysis on multiple groups.
Regards
Yogender Kumar Gowtham
Graduate Research Assistant
Clemson University
Department of Bioengineering
202 Biosystems Research Complex
Clemson, SC
(864)650-7451
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