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Puhong Gao
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140
@puhong-gao-116
Last seen 10.2 years ago
Hi, all,
I'd like to background correct my data using sequence info and then to
explore them with different normalization algorithms, vsn and
quantiles, for examples. Has anyone ever tried it this way? Can
someone give some suggestions of how to do that? Thank you in advance
for your help.
I performed background correction of my data using "bg.correct.gcrma"
function and used "expresso" function to normalize (quantiles) the
data without background correction. To my surprise, the normalized
intensities from this procedure are quite different from the
intensities generated with gcrma function (default parameters). Using
separate bg correction seems to generate many extremely small
intensities (~ -9 of log2 value). Is there anything wrong of what I
have done?
Best,
Puhong Gao, PhD
Dev. Psychobiology
NYSPI, Unit# 40
1051 Riverside Dr.
New York, NY 10032
(212) 543-5710
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