Hi Iain,

Can you paste your code for romer, the design matrix and the contrast you
are interested in?

I suspect the contrast has not been the one you are interested in.

Cheers,
Di

On Tue, Nov 30, 2010 at 5:05 AM, Iain Gallagher <
iaingallagher@btopenworld.com> wrote:

> Hello list.
>
> I have a quick question about the 'romer' function used for GSEA in the
> limma suite.
>
> With guidance (much appreciated!) from Di Wu I have run some data through
> the algorithm and the results look appropriate for my dataset.
>
> The question I have is to do with the p-values returned. I run romer with
> 9999 rotations (a method suitable for 'permutation' in linear models) and
> get back ~3200 sig genesets. This is from an examination of ~ 17000 probes
> across 2 groups (3 adult arrays and 9 fetal arrays - affy data).
>
> If a set is significant I get back a p value of 0.0001 - nothing more &
> nothing less. If a set is not sig I get a p value of 1.
>
> I understand that the MINIMUM p value is 1/(nrot+1) so all my significant
> sets are at the minimum p value.
>
> I would have expected a range of p values however. Could someone with a
> more statistical background shed some light on this? Perhaps my groups are
> very different (would make some sense I suppose).
>
> Thanks again in advance for any help.
>
> iain
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>  [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] hgu133plus2.db_2.4.5 org.Hs.eg.db_2.4.6   RSQLite_0.9-3
>  [4] DBI_0.2-5            AnnotationDbi_1.12.0 genefilter_1.32.0
>  [7] hgu133plus2cdf_2.7.0 affy_1.28.0          Biobase_2.10.0
> [10] RColorBrewer_1.0-2   limma_3.6.6
>
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0         annotate_1.28.0       preprocessCore_1.12.0
> [4] splines_2.12.0        survival_2.36-2       tools_2.12.0
> [7] xtable_1.5-6
> >
>
>
>
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