huber at ebi.ac.uk
Mon Jun 5 18:57:36 CEST 2006
I am surprised why anybody is surprised about the different number of
modes ("peaks"): the number of modes of a distribution is not conserved
under monotonous transformations (such as the background correction in
RMA), this simply follows from chain rule.
See below for a simple example with some "mock" microarray intensities z
and density of log-transformed values before and after a (primitive)
background background correction.
n = 100000
z = 20 + exp(c(rnorm(n), 3+rnorm(n)))
noel0925 at sbcglobal.net wrote:
> In the paper: Exploration, Normalization and Summaries
> of High Density Oligonucleotide Array Probe Level Data
> the following statement regarding the
> bimodality of log2(PM) values and RMA background
> corrected PM values can be found- "The same bimodal
> effect is seen when we stratisfy by log2(PM), thus it
> is not an artifact of conditioning on sums." (p4).
> I am a little confused by this as I thought that
> indeed an artifact of the convolution!
> Clearly, the background corrected intensity
> values are given by E(S | O) or the conditional
> expectation of the signal given what we observe; where
> the observed signal is the convolution of a normally
> distributed background (N) mean mu variance sigma^2
> (B~ N(u, Ïƒ^2)) and an exponentially distributed
> signal (S) with mean alpha (S~ exp(Î±)).
> There have been several postings regarding this matter
> in the Bioconductor archives and all seem to point to
> this. Have I misunderstood?
> In particular was the following post:
> (See below the response from zwu at jhsph.edu
> The original question I got was about the bimodal
> distribution of gcrma
> result from probe intensities with unimodel
> distribution. My answer was
> that the "change" was not necessarily surprising.
> For example , when you have "true log signal" from a
> bimodal distribution
> # You will see this has two peaks
> #if the background, log(non-specific binding) come
> #then when you plot the histogram of convolution in
> log scale,
> #you see only one peak, and this would be "before
> This explanation made sense to me, but seems to
> contradict what is stated in the paper.
> Also, can someone explain the difference between RMA
> background version1 vs version2?
> Best regards,
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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