[BioC] Affy package ?s (sorry for the repost)

Ben Bolstad bolstad at stat.berkeley.edu
Thu Mar 20 09:19:00 MET 2003

> Question 1: Are the values output by rma to eset (and written to tab
delimited file with write.exprs) the logbase2 of the "actual" affyID
values, or are they the affyID values themselves. This is obviously
important for comparing rma to our old methods, and for estimates of
"accurate" fold change estimates- It seems to me that rma is much more
precise in that much of the noise between replicates, especially at the
low end, seeems to have been reduced in rma, but I am struggling with
how to estimate back to accurate fold change estimates.

The values given by the rma() function are log base 2. Working in log
base 2 you could take differences and then take 2^(difference) to get
fold changes. Or you could just take 2^(rma expression value) and take
ratios if you prefer.

You might find that RMA estimated fold changes are attenuated compared
to other methods. That is that the estimated fold change is smaller than
that computed using other methods. But the noise reduction at the low
end is pretty dramatic.

> Question 2: Is there an easy way to write out the PM values to tab
delimited file post background correction and normalization (to assess
individual probe sets prior to median polish). I am trying to work out
reasons for differences between our old method and rma for individual
affy IDs.

If you manually background correct and normalize (as individual steps),
doing something like

data <- ReadAffy()
data.bg <- bg.correct.rma(data)
data.norm.bg <- normalize(data,method="quantiles")

in each case pm(data.bg) and pm(data.norm.bg) will give pm matrices
after preprocessing. Investigate the function write.table() for
outputting the data to tab delimited files.



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