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Shinhan Shiu
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60
@shinhan-shiu-1172
Last seen 10.2 years ago
I am working on Arabidopsis tiling array data. I want to adjust the
intensity based on GC content then do normalization. But the CDF and
CEL
files are not available so the sequences and raw intensities are
downloaded
from Gene Expression Omnibus instead.
I have extracted codes from gcrma and the hacked version works fine
for
background correction and affinity adjustment. I run into trouble,
however,
when I try to do quantile normalization.
The method "normalize" takes an affyBatch object but I am working with
a
matrix of numbers. I wonder if there is any work around or other
methods I
can use.
Shinhan
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Shinhan Shiu
Dept. of Ecology and Evolution
University of Chicago