Looking for the best software to do microarray image quantitation

Patrick in_vivo at usa.net
Fri Apr 5 03:31:24 EST 2002

Hi, recently I came to do some gene expression profiling using the
house-fabricated glass microarray chips. At our college, they use some
commercial software to "automatically" process hundreds of chips after

The concern here is that I was in a class project about one and half
years ago to compare the processed results using different software
with the same scanned microarray image. The results were so
disappointing that the two results were dramatically scattered.

So I'm looking for some expert advice about which image quatitation
software, either from academia or commercial ones, is the "best" so
far in the world. Well, on the other side, it's hard to define the
"best" software. Because we don't know what the "true" signal
information is, I think a "good" software should be consistent with
its own automatic and manual detection and quantitation. I also prefer
a program or a group of software that generate REPRODUCIBLE results
cross platform/software for the same image. I don't expect too many
fancy analysis functions. I think a decent software should just get
the job done well, which is extracting as faithfully as much
information of the signals from the scanned images. The only thing we
need is "good" raw data.

I can't find any resources or literature that provide me with this
kind of information, so I come on here to ask for advice.

Thank you.


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