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IV. Measurement and data processing
A. Data Extraction
Image scanning and software
Procedures and parameters
Hybridized arrays were scanned with
ScanArray 4000 (Packard Biochip technologies, Inc. USA) at laser intensity
and photomultiplier tube voltage setting giving the best dynamic range for
each chip in the two channel, the ratio of the mean signal intensities was
~1, and the percentage of spots with saturated pixels was <0.25% but >0%.
Image segmentation and spot local background quantification was performed
with analysis software GenePickPro 3.0 (Axon Instruments, Inc. USA).
Raw data
See the file Raw
Data
B. Normalization
Software: Rowless
(www.jax.org/staff/churchill/labsite/software/anova/rmaanova)
Results
of normalization
C. Cutoff determination
Cutoff determination
D. Differentially
expressed ESTs
Differentially expressed ESTs
E. Clustering
Software: Self-Organizing Maps (SOM)
Results
of clustering
F. GO analysis
Databases for gene annotation
http://www.geneontology.org
http://www.ebi.ac.uk/swissprot
