Entering edit mode
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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