Hi,

This is a conceptual question related to microarray, instead of the usage of
any Bioconductor package. I apologize if this bothers anyone.

I am struggling to understand the concept of differential expression in
terms of its resources (whether it is technical or biological). Suppose I
have an experiment with two groups (healthy vs. disease) and try to find
some differentially expressed genes, take two genes for example, both of
them are differentially expressed (DE) between healthy and disease.

Gene A has present detection call for all the samples under study (but the
detection call p-value in the healthy group is in the order of 1e-2 ~ 1e-3,
the detection call p-value in the disease group is much more significant
(say, 1e-10)).
Gene B has 50% present call in healthy while 100% present call in cancer.

My question is what's the correct interpretation in terms of whether the
differential expression is due to technical or biological? Are they both DE
due to technical, or A is DE due to biological and B is due to technical, or
they are both DE due to biological?

Thanks a bunch,

-Jack

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