[BioC] A couple of questions

Ali Al-Timimi aaltimim@gmu.edu
Mon, 30 Sep 2002 15:53:24 -0400

Hello everyone,

I would like to first to thank you all for providing such a great service.
I've download the code base and played around with it, but I have a couple
of straightforward questions.

I am trying to load my own data but I am unsure as to what format(s) I
should place it in. I have 2-colored cDNA and I have seen the swirl data you
have provided but I am not certain if I have to map my data to that format.
Here at George Mason University, we use QuantArray so our data comes out
with the following format:

>Number    Array Row    Array Column    Row    Column    Name    X Location    Y
>Location    ch1 Intensity    ch1 Background    ch1 Intensity Std Dev    ch1
>Background Std Dev    ch1 Diameter    ch1 Area    ch1 Footprint    ch1
>Circularity    ch1 Spot Uniformity    ch1 Bkg. Uniformity    ch1 Signal Noise
>Ratio    ch1 Confidence    ch2 Intensity    ch2 Background    ch2 Intensity Std
>Dev    ch2 Background Std Dev    ch2 Diameter    ch2 Area    ch2 Footprint
>ch2 Circularity    ch2 Spot Uniformity    ch2 Bkg. Uniformity    ch2 Signal
>Noise Ratio    ch2 Confidence    Ignore Filter

My second question is I would like to have the classes you have created read
directly from my database if possible. Do you have any suggestions as to how
that can be approached?


Ali Al-Timimi
Graduate Student
Center for Biomedical Genomics and Informatics
George Mason University