[BioC] log2 ratio as limma input

[Gordon K Smyth]

> Date: Fri, 16 Jun 2006 09:07:52 -0700 (PDT)
> From: yuhong ning <yhning at yahoo.com>
> Subject: [BioC] log2 ratio as limma input
> To: bioconductor at stat.math.ethz.ch
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi,
>
> I am trying to use limma to analyze Mass Spec data for
> differentially expressed proteins from wild type cell
> and mutant cells. The input data I got from scientists
> is the intensity ratio of Heavy-isotope/light-isotope
> peptide. I want to read it into MAList, but seems the
> ratio data only correspondent to M, I have no way to
> obtain the "A" data. What should I do?
>
>
> Thanks a lot.
>
> yuhong

Dear Yuhong,

All the limma commands you might want to use accept simple matrices as input, so I can't think of
any reason why you would need to read you data into an MAList object.

Best wishes
Gordon