[BioC] DE in edgeR

[Gordon K Smyth]

Dear Robin,

Please read the posting guide:

   http://www.bioconductor.org/help/mailing-list/posting-guide

In particular, you should "Ensure that your installed packages are 
up-to-date" by installing the most recent release of Bioconductor.  Your 
software is at least a couple of releases out of date.

As you may have realized, your experiment has no replication.  If you want 
to ignore the time points (treat them as replicates), then your experiment 
reduces to a simple two group problem, and the edgeR User Guide provides 
plenty of advice on how to do that.  As the posting guide says, "Read the 
relevant R documentation".

However, there are better ways to analyse your data.  Are you open to a 
more sensible suggestion?

Best wishes
Gordon

> Date: Thu,  1 Nov 2012 03:38:53 -0700 (PDT)
> From: "R [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, robinmjelle at gmail.com
> Subject: [BioC] DE in EdgeR
>
>
> I am testing DE between two groups that each contain 10 time points.
>
> I am creating my design matrix like this:
>
> Condition <- factor(c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT","WT","WT","WT","WT","WT","WT","WT","WT"))
> Condition <- relevel(Condition, ref="WT")
> Time <- factor(c("0H","3H","6H","9H","12H","18H","21H","24H","27H","0H","3H","6H","9H","12H","18H","21H","24H","27H"))
>
> design <- model.matrix(~Time+Time:Condition)
>
>
> How do I proceed if i want to compare the whole group (WT) against the 
> other group (KO) considering the time points as replicates.
>
>
>
> -- output of sessionInfo():
>
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=nb_NO.UTF-8       LC_NUMERIC=C               LC_TIME=nb_NO.UTF-8
> [4] LC_COLLATE=nb_NO.UTF-8     LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=nb_NO.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.2.1   DESeq_1.6.1           locfit_1.5-8          org.Mm.eg.db_2.6.4
> [5] RSQLite_0.11.2        DBI_0.2-5             AnnotationDbi_1.16.19 Biobase_2.14.0
> [9] edgeR_2.4.6           limma_3.10.3
>
> loaded via a namespace (and not attached):
> [1] annotate_1.32.3    genefilter_1.36.0  geneplotter_1.32.1 grid_2.14.1
> [5] IRanges_1.12.6     lattice_0.20-0     RColorBrewer_1.0-5 survival_2.36-10
> [9] tools_2.14.1       xtable_1.7-0


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