[R] Help needed to analyse a factorial microarray experiments! Newbie Question
Leonardo Boava
leoboava at yahoo.com.br
Tue Feb 26 13:35:23 CET 2008
Dear R-users:
I am using the package MAANOVA to analyze microarray data and have
encountered problems when trying to get interactions.
I am a newbie in both, R and maanova, and I do not have good knowledge in
statistical methods.
I have four effects:
Effects Levels
Var 2
Ind 2
Trat 2
Time 4
Sample 3 <-- biological replicate
Spot 4 <-- technical replicate
I had fitted a model to got all interactions with Samples in random effect
(mixed). But, I got an error when I include the Var:ind:Trat and Var:ind:Time
in the fitted model. May be I didn't had degree of freedom enough.
Then I did an analyses without those interactions (Var:ind:Trat and
Var:ind:Time ).
Now, I would like to known if are possible to get the interactions with three
factors and interactions with four factors.
I am interested in known which genes are differentially expressed in Var 1,
Ind 2, Trat 1 , Time 3, for example.
Could you address me how do I could do that?
If I include the technical replicate in the model, can I get those
interactions?
If you had analysed a experiment like this, could you share your script?
Does anyone have experience using MAANOVA commands and is willing to help?
Any comments are very welcome!
Thank you very much.
Leonardo
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