[BioC] Discrepancy on results from gcrma function and justGCRMA
jzhang at vapop.ucsd.edu
Wed Oct 28 23:31:36 CET 2009
Jerry <norn2k at ...> writes:
> I'm currently using gcrma package in R to summarize probeset intensities from
CEL files. Surprisingly,
> I found that the results generated from gcrma function and justGCRMA function
are quite different. In
> general, expression values from gcrma function are lower and the boxplots from
gcrma are quite
> asymmetric (no tails on the bottom). I attached some plots below for your
information. This confused
> me as I thought that the two functions implemented similar algorithms.
> Thank you so much for your help!
> PS: The package I used is gcrma 2.12.1. I also observed similar results
on 2.14 version.
I'm running into the same problem with gcrma and justGCRMA. They are not giving
the same numeric results. Is this an intended feature?
I was under the impression that these two methods were identical with the
exception that justGCRMA was more memory efficient because it didn't have to
create an AffyBatch object.
Can anyone shed some light on this subject?
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