[BioC] limma: decideTests

[Al Ivens]

Hi all,

I am doing some analyses of Affy arrays using limma.  Following the
manual, I generated the fit2 object using the default eBayes settings,
and topTable with (almost) default settings. 

> dim(eset)
Features  Samples 
   22625       15 
> fit <- lmFit(eset,designMATRIX)
> fit2 <- eBayes(contrasts.fit(fit,contrast.matrix))
> TT <- topTable(fit2,adjust.method="BH",number=length(fit2$genes))

I am now using decideTests, and have read the help that goes with it.
However, I still can't decide (no pun intended) on what is the best
method ("separate", "global", "hierarchical", "nestedF") to apply with
what adjust.method ("none", "BH", "fdr", "BY", "holm"). I have so far
left adjust.method as "BH", and varied the method.  I can chose one
(global) that gives me most of the genes I "want", but I'd rather chose
the method more objectively.  I have 5 contrasts, so am guessing from
the email archives that nestedF is probably not appropriate for so few
contrasts?

Are there any general guidelines as to which is the best method to use
when?

Thanks in anticipation,

a


> sessionInfo()
R version 2.6.0 (2007-10-03) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils
datasets  methods   base     

other attached packages:
 [1] statmod_1.3.1             celeganscdf_2.0.0
arrayQualityMetrics_1.2.0 latticeExtra_0.3-1        CCl4_1.0.6

 [6] simpleaffy_2.14.05        affyPLM_1.14.0            gcrma_2.10.0
matchprobes_1.10.0        RColorBrewer_1.0-2       
[11] vsn_3.2.1                 genefilter_1.16.0         survival_2.34
geneplotter_1.16.0        lattice_0.17-2           
[16] annotate_1.16.1           xtable_1.5-2
AnnotationDbi_1.0.6       RSQLite_0.6-4             DBI_0.2-4

[21] celegans_2.0.1            affy_1.16.0
preprocessCore_1.0.0      affyio_1.6.1              Biobase_1.16.1

[26] limma_2.12.0             

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-21




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