[BioC] replace negative values in Agilent miRNA data

Wolfgang Huber huber at ebi.ac.uk
Wed Oct 29 14:59:14 CET 2008

Hi Christian,

this question is discussed (and IMHO, answered :) here:
and also in a somewhat more pointed form in sections 3.2+3.3 of

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

24/10/2008 16:33 Christian Eisen scripsit
> 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

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