in_vivo at usa.net (Patrick) wrote in message news:<db4f87f8.0204041831.5f7a9eae at posting.google.com>...
> 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
> scanning.
>> 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.
>> ---
Have you tried
http://www.wehi.edu.au/bioweb/NatsStuff/microarray2.html
which is one page from The Walter & Eliza Hall Institute of Medical
Research (Melbourne,Australia) Web Resources for Microarrays. It also
refers to
http://www.stat.berkeley.edu/users/terry/zarray/Html/
which is Terry Speed's Microarray Data Analysis Group Page
at Berkeley. Terry Speed has a joint appointment as Professor at
Berkeley Stats. Dept. and Head of the Bioinformatics & Genetics
Division at The Walter & Eliza Hall Institute,
cheers,
Keith Satterley
The Walter & Eliza Hall Institute of Medical Research
Melbourne,
Australia
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