[BioC] normalization of duplicate spots
Jianping Jin
jjin at email.unc.edu
Fri Feb 17 16:30:52 CET 2006
Dear BioConductor list:
I have a set of one color (cy3) data in which each gene was spotted
duplicate in separate blocks (grids). I looked at how well the duplicated
genes were correlated by using either "duplicateCorrelation" (limma) or
regular "Pearson" correlation test. Both tests gave out similar values
around 0.55.
Duplicate spots should be highly correlated in intensities. The correlation
coefficient of 5.5 is not that great as I understand. Limma has some ways
to process those technical replicates, such as "print-tip loess" and
incorporating estimated spatial correlation into analysis using generalized
linear model. But what if I just wanted to preprocess data with something
like vsn or IQR normalization without using linear model fit? Should I
normalize the grids, e.g. grids 1 and 3, grids 2 and 4 (which contain
corresponding duplicate spots) on each chip to make duplicate spots more
correlated?
Usually I just get mean values of the duplicate spots for such a small data
sets (722 genes on each slide). Does anybody know a better way to handle
these duplicates than using means? I will greatly appreciate if anyone
could share her/his experience with me!
Thanks in advance!
Jianping
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x Jianping Jin Ph.D. x
x Bioinformatics scientist x
x Center for bioinformatics x
x 3133 Bioinformatics Building x
x CB# 7104 x
x University of North Carolina x
x Chapel Hill, NC 27599 x
x Tel: (919)843-6105 x
x Fax: (919)843-3103 x
x E-mail: jjin at email.unc.edu x
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