[BioC] Significant dye bias using limma

[Mark Pinese]

Will such a significant bias affect the validity of my treatment effect 
results?  In other words, can I just appreciate that dye bias is 
rampant, then ignore it and confidently extract meaningful statistics 
from my treatment vs control coefficient?

Mark


Gordon K Smyth wrote:

>The fact that the dye effect is often highly significant is the reason that it is recommended to
>include it in the model.
>
>Gordon
>  
>
>>
>>Is such a strong result plausible, or due to me incorrectly analysing the data?
>> If so, what major pitfalls could I have blundered into?  What sort of
>>diagnostics can I try to test how reliable the model results are?
>>
>>    
>>