Dear list, 

 

I am analizing some data that come from a paired experiment: control vs
treatment are compared within a given slightly different sort of cells (as
if they were different batches of raw material) 

I have 3 levels for the cell effect (block effect), and I compare the
control vs treatment at each level of the block effect, so 6 arrays. Using
limma, I write the model: 

 

y = treatment + block + error  

 

and after estimating the treatment effect,  I do the contrast: 

 

control – treatment. 

 

My cuestion is:

 

Given this model, if I decide to eliminate an array, say a control in one of
the levels of the block (I think that this array could have had some
hibridization problem according to some QC analisys), would it be still
possible to estimate the treatment effect correctly? 

 

I think that the level of the block from where I picked the array off will
be confounded with the treatment effect, and  I am not sure if the contrast
control – treatment would give me the list of DE due to the treatment effect
or due to something else?.- Would be more correct to eliminate the whole
block? 

 

In my case, if I eliminate the whole block I end up with only 4 arrays that
decrease the power of the analysis. 

 

I would appreciate any comment on this.- 

 

Thank you very much.- 

 

 

Pedro 

 

 

 

 


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