[BioC] replace negative values in Agilent miRNA data

[Christian Eisen]

Hello everyone,

as some of you may be familiar with Agilent's miRNA Array, the intensity 
files the
Agilent Feature Extraction Software delivers contain negative values.
These result from the background being substracted from the spot 
intensity and if
the background is higher than the spot (i.e. no gene detected) it gets a 
negative value.
Needless to say, log-transformation is not working on these.

So therefore I came up with an alternative to make log-transformations work.
I replaced all negative values in my data with the smallest positive 
value in my data
something like 0.00103.
However, as you already might expect, upon log2-transformation, this 
value becomes really small (almost -10)
Still there are non-manipulated intensity values in my data being as small.
So my question is, if this is correct if I replace negative values by a 
very small positive value or not?
Upon analysis of differential expression, I get genes which are enriched 
in these manipulated values in
either of the two groups I concider.
But my justification for doing this is, if a gene has a negative value, 
i.e is not detected, there should be a significant
difference, concidering a large enough intensity in the group compared 
to, between the two.

Am I wrong on this?

Thanks !
Christian