[BioC] adjusted p-values for large number of genes...

Lourdes Peña Castillo lourdes.pena at gmail.com
Thu Aug 11 00:41:17 CEST 2005


I am using  limma to select differentially expressed genes. I have 24
arrays and 40k genes. According to the limma users' guide, "If none of
the raw p-value are less than 1/G, where G is the number of genes,
then all of the adjusted p-values will be
equal to 1". 

I get raw p-values which are less than 1/G after applying eBayes;
however, the lowest adjusted p-value I get using "fdr"  is 0.66. Does
that mean that I cannot adjust for multiple testing in experiments
involving  many genes?   Should I then use an arbitrary cut-off on the
raw p-values? or what are the alternatives?



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