[BioC] technical + biological replicate design for multiple categories

[James Platt]

On Jul 3, 2013, at 1:32 PM, Naomi Altman wrote:

> You need to have a variable "biorep" with biorep number e.g. c(1,1,2,2,3,3,...6,6)
> 
> This is a blocking variable.

So I have to use numbers for the blocking variable? I can't use text?  Otherwise, it's the same as the variable which I called "block."  

> The treatments are just Cyt1, Cyt2 and Mock.

My design matrix should have just those three columns?  Then, my variable "treatment" should actually be the following:

treatment <- c("Mock", "Mock", "Cyt1", "Cyt1", "Cyt2", "Cyt2", "Mock", "Mock", "Cyt1", "Cyt1", "Cyt2", "Cyt2")


> You will need to follow the instructions for blocking variables.

If I understand the user guide correctly then it's the same as what I did before except for having the corrected "biorep" and "treatment" variables:

design = model.matrix(~ 0 + treatment)
dupcor = duplicateCorrelation(expr, design, block=biorep)
fit.raw = lmFit(expr, design, block=biorep, correlation=dupcor$consensus)
fit = eBayes(fit.raw)

This runs without error but I just want to make sure that it's correct.  The results do make sense.  In other words, the top ranked genes include many that were expected.

Thanks,
James