Dear Dr. Smyth,

 

I have "two groups Affymetrix" experiment with 5 biological replicates
in one group and 2 technical replicates in other. In other words one
group has all biological replicates and the other has all technical
replicates. I would really be thankful to know how to use LIMMA (to
identify differentially expressed genes) for such kind of design. 

 

After reading LIIMMA user's guide and your post on [BioC] on "defining
and handling replicates", the code appears to be written in following
way:

 

design <- cbind(disease=c(1,1,1,1,1,0,0),control=c(0,0,0,0,0,1,1))
corfit <- duplicateCorrelation(eset, design, ndups=?, block=c(???))
fit <- lmFit(eset, design, block=c(???), correlation=corfit$consensus)

 

But how do I write block and ndups? 

 

Your help is really appreciated.

 

Thanks and Regards,

--

~Nikhil Garge

3040 Cornwallis RD

Durham NC 27709

Research Triangle Institute [RTI}

Email: ngarge@rti.org

 

 

 

 


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