[BioC] Agilent microarray

s-uchida s-uchida at jaist.ac.jp
Mon Jul 26 17:54:20 CEST 2004


I have been processing Agilent long-oligo (60-mer) microarray data.  

After scanning the microarray slide, I used ScanAlyze to convert the image
into numerical data.  Then, I applied Total Intensity Normalization and
LOWESS to normalize the data.  

However, the MA-plot after the normalization indicated that the data points
at the higher A-value deviate from the M = 0 line.  The whole plot looks
like a flying bird with its beak pointing towards the lower edge of the
plot.  After examining the scanned image of the data, I found that most of
these deviated data points were growing yellow.  Thus, it should not affect
the further analysis of this data, but I am curious to know if anyone has
ever seen something like this.  Is this typical for Agilent microarray data?

Thank you.


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