[BioC] Limma and Block Effects
Pie Muller
pie.muller at liverpool.ac.uk
Mon Sep 26 16:19:55 CEST 2005
Hi Bioconductors
I followed the example 10.2 in Limma's user guide which includes a
coefficient for each mouse in the linear model to account for technical
replication. I am somewhat puzzled because the example in the user's guide
returns non-estimable coefficients and hence the contrast (mu1+mu2-wt2)/2
as proposed in the guide cannot be computed... (I assume the function
"designMatrix()" can be replaced by "modelMatrix()".) Since the given
example returns an error, and I am not a statistician, I am struggling in
finding the correct solution. As we have four replicate spots on our
arrays I cannot use the "duplicateCorrelation()" function here. How does
the correct design matrix look like and which contrasts need to be computed?
Has anyone a solution either for the example given in the user guide or my
own experiment listed below?
MANY THANKS!
Pie
I have 3 biological replicates and two technical replicates for each
biological replicate, i.e.,
FileName Cy3 Cy5
File1 A1 B1
File2 B1 A1
File3 A2 B2
File4 B2 A2
File5 A3 B3
File6 B3 A3
and would like to estimate the effect between A and B including a
coefficient to fit a separate effect for each individual.
More information about the Bioconductor
mailing list