[BioC] A couple of questions

[Ali Al-Timimi]

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?

Sincerely,

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