[BioC] basic limma questions

[Gordon K Smyth]

Dear Endre,

It sounds as if limma recognised the ArrayVision format fine.  As far as I 
know, there is no way to tell from the ArrayVision file which channel is 
cy3 and which is cy5.  Even though limma got them the wrong way around in 
this case, it doesn't really matter because it makes no difference to the 
analysis.  The Data-Ctrl contrast is the same regardless of which is R and 
which is G.

Best wishes
Gordon

On Mon, 31 Mar 2008, Endre Sebestyen wrote:

> Thanks for your answer. A little more details :
>
> I had a control and a treatment, with 3 technical replicates and no
> dye-swaps. Cy3 was the treated, Cy5 the untreated.
>
> The ArrayVision result file looks like this :
>
>                                 Ctrl    Ctrl    Ctrl    Data    Data
>  Data
> Spot labels     VOL - MDC       Bkgd    sVOL    VOL - MDC       Bkgd
> sVOL    Ratio (sVOL):  Data / Ctrl      Diff (sVOL):  Data - Ctrl
> MZ00023554 - TC248295 (1)       87573.5998      29969.817
> 57603.783       51217.7619      15349.622       35868.140       0.623
> -21735.643
> MZ00023408 - TC248006 (1)       29389.2252      29831.153       0.000
> 15896.2700      15349.622       546.648 1.0000e+100     546.648
>
> I extracted the ID, Ctrl VOL, Ctrl Bkgd, Data VOL, Data Bkgd columns.
> When I used the read.maimages function, Ctrl VOL became R, Data VOL
> became G, Ctrl Bkgd became Rb, DataBkgd became Gb.
>
> Endre
>
>> > Date: Fri, 28 Mar 2008 12:51:39 +0100
>> > From: "Endre Sebestyen" <endre.sebestyen at gmail.com>
>> > Subject: [BioC] basic limma questions
>> > To: Bioconductor <bioconductor at stat.math.ethz.ch>
>> >
>> > First, limma didn't recognize the ArrayVision format, and I had to
>> > parse the raw data and define the columns myself. Is it correct to
>> > pass the CtrlVol to R, DataVol to G, etc?