Hallo again,

thanks for the help. I have found out that the experiment was done with a
common reference. So if i understand it correctly I have here the first
option you mentioned.

so I gues my design matrix should looks like that:

wt c1 c2 c3 c4 c5 c6
1 0 0 0 0 0
0 1 0 0 0 0
0 0 1 0 0 0
0 0 0 1 0 0
0 0 0 0 1 0
0 0 0 0 0 1

and my contrast.matrix something like that

wt c1 c2 c3 c4 c5 c6
-1  1  0 0 0 0 0
-1  0  1 0 0 0 0
 0  -1 0 1 0 0 0
 0  -1 0 0 1 0 0
 0  0 -1 0 0 1 0
 0  0 -1 0 0 0 1

if i want to compare the first two with the control, number c3 & c4 with c1
and number c5 and c6 with c2

Do I need to also do a within-array normalization on this data set?

Thanks
Assa

On Tue, Jul 31, 2012 at 12:51 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Mon, Jul 30, 2012 at 10:55 PM, Assa Yeroslaviz <frymor@gmail.com>wrote:
>
>> Hi, Sean,
>>
>> yes I know that. Unfortunately the biologist is not exactly next to me, as
>> it is a collaboration.
>>
>
> A lot of us work on collaborations like this.
>
>
>> Well, I asked for the protocol. maybe I can figure it out.
>>
>> What I would like to know is, whether it is possible to do a two-channel
>> hybridization protocol with just one biological probe on the array. Does
>> it
>> make sense at all?
>>
>>
> There are four possibilities, at least:
>
> 1)  Two color hyb, two color scan
> 2)  Two color hyb, one color scan
> 3)  One color hyb, two color scan
> 4)  One color hyb, one color scan
>
> It sounds like your data have both colors in the output file, so either 1
> or 3 was done.
>
>
>> If so, what happened in the 'second' channel? Do I need to take both
>> channel under consideration?
>>
>
> This is the question you need to turn back to your biological
> collaborator.  We cannot answer this question, unfortunately.
>
>
>>
>> If there is only one probe, will it spread onto both channels?
>>
>>
> The two channels are from the same probe.  As I mentioned above, if you
> have two channels worth of data, there are at least two explanations.
>
>
>>  thanks again,
>>
>> Assa
>>
>> On Mon, Jul 30, 2012 at 9:04 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
>>
>> >
>> >
>> > 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
>> >
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>

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