[BioC] Analysis: two-color, time series

[Gordon K Smyth]

Dear Olga,

   Time <- factor(targets$Cy5)
   design <- model.matrix(~Time)

Best wishes
Gordon

> Date: Thu, 5 Aug 2010 00:41:13 -0600
> From: "Olga K. Kamneva" <kamushkina at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Analysis: two-color, time series
> Content-Type: text/plain
>
> Dear List,
>
> I need help with the analysis of time series experiment. I have cDNA
> microarray data produced with genepix.
> Bacterial cells were induced for sporulation (3 biological replicates), RNA
> was extracted from cells before induction and after 1,2,3 and 4 hours after
> induction. RNA from uninduced cells was labeled with Cy3, from respective
> induced cells with Cy5 and hybriduzed onto two-color microarray.
> To summarize the data:
> # biol repl     Cy5    Cy3
> 3                 1h       unind
> 3                 2h       unind
> 3                 3h       unind
> 3                 4h       unind
>
>
> How should I analyze this data to find differentially expressed genes?
> I am trying to use limma package, but I cannot come up with proper design
> matrix  to fit the linear model.
>
>
> I will very much appreciate any help, as I am not very experienced
> microarray data analyst.
>
>
> Thank to everyone,
> Olga.

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