[BioC] Single channel array, limma and imagene

[James W. MacDonald]

Hi Carla,

On 12/6/2010 8:15 PM, Carla Zammit wrote:
>
>
> Hi All,
> I am new to microarray analysis but have spent some time trying to solve/research my problem but as yet have not prevailed.
> I have inherited some single-channel microarray data produced using Imagene, I have tried to find a good workflow to do annalyze the data but have been unable to find something that works for the Imagene data files.
> Has anybody dealt with single-channel Imagene data using Limma before, if so can you point me in the right direction? (I have searched through the archives, have the Limma manual and a couple of the recommended text) If there is no guide available I will post my script and hopefully someone can help.
> Thank you.

I think you will need to give more information than that. Imagene is one 
of the platforms that are directly targeted by this package (see e.g., 
?read.imagene), and there are arguments to that function specifically 
for single-channel data.

In addition, starting on p. 31 of the limma User's Guide, there is 
information about handling single-channel data.

If you can give specific things that are confusing to you, perhaps 
someone can help.

Best,

Jim


> Regards,Carla
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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