[BioC] Imaging of Protein Array

[Jordi Altirriba Gutiérrez]

Dear Uchida,
I tried to analyze a similar protein array.
You can have a look to:
https://stat.ethz.ch/pipermail/bioconductor/2006-June/013311.html

What I did was to invert the black and the white image, so that the spots 
appear in white and the background in black and I analyzed the images as if 
they were a Cy3 image with the commercial program GenePix.
There are another programs to obtain the signal intensity and the background 
(GridGrinder {free} [http://gridgrinder.sourceforge.net/], SpotFinder 
{free}[http://www.tm4.org/spotfinder.html], Spot {free 1 
month}[http://spot.cmis.csiro.au/spot/index.php],
).

About Spot, which has been recommended, I didn’t find how to manage with 
“one channel” arrays, as the protein arrays (perhaps I am wrong).

There is also an R package (apart from Spot), which is Spotsegmentation, 
although I don’t know how to manage it, and there was some mails asking 
about it without any answer.

I recommend you that you have a look to:
http://ihome.cuhk.edu.hk/~b400559/arraysoft_image.html
Although it’s a little bit out of date (2004), it’s quite useful.

HTH,

Jordi Altirriba
PhD student
Hospital Clinic, Barcelona, Spain

>Hello.  I am trying to convert the tiff images of RayBio Cytokine Antibody 
>Array (http://www.raybiotech.com/product.htm) into numbers in order to 
>compare them numerically.
>The problem I am having now is that how to define the area of a spot.  Do 
>any of you have experience with working with protein arrays?  Any help is 
>appreciated.  Thank you very much for your help in advance.