On Mon, Jul 30, 2012 at 2:49 PM, Assa Yeroslaviz <frymor@gmail.com> wrote:

> Hi everybody,
>
> I have a data set of Agilent CGHArray. I would like to know whether
> these arrays were made with the two-chanel or one-channel protocol.
> When I look at the results from the Agilent FE files, I can see both
> g- and r-signals (eg. g(r)BGSubSignal, g(r)Median etc.)
> Asking the biologists I was told, that they are interested in the
> gBGSubSignal column of the results file. What I understand from that
> is, that the experiments ware made as single-channel exp.
> Is there something like that - a one-color experiment with a 2-color
> hybridization protocol?
>
> What kind of data do one has on the red channel, if this is really is
> a 1-channel experiment?
>
> As they also did one array with control (unchanged cell lines), I
> really think this is 1-channel arrays. Do you need a separate control
> experiments for a two-color arrays?
> Is it possible, that the red channel is some kind of a reference
> independent of the cell lines?
>
>
Hi, Assa.

Your best bet is to sit down with the biologists who designed and ran the
experiment to describe the experiment and the protocols used to produce the
final data.  Only then can you really understand what they want and how
best to get that to them.

Sean

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