Hi all,

I was doing an RMA->limma (ebayes) analysis of an affymetrix mouse 430a
experiment and noticed that while the p-values listed in toptable were all
different, the adjusted p-values (adjust="BH") contained duplicate values.
 I don't think this is incorrect necessarily, but I was wondering why a
different alpha wasn't generated for each gene.  From what I understand, the
BH method gets the adjusted p-value (alpha) from [P_k*n*c(n) ] / k < alpha,
where n = total number of genes (tests), P_k = p-value at kth gene (genes
ordered from low to high p-value), and k = number of genes with p-value less
than or equal to P_k.  I'm not entirely sure how the c(n) (dependence
correction) part works, but it seems like a unique adjusted p-value (alpha)
could be generated for each gene.  Instead I get:


>top<-topTable(efit, adjust="BH", n=nrow(exprs(rmadata)))
>write.table(top, "output.xls", sep="\t")

from output.xls...
 ID                   adj.P.Val           P.Value
 Mm.277921    0.039259664     3.17E-06
 Mm.272646    0.050424143     9.93E-06
 Mm.148886    0.050424143     1.64E-05
 Mm.235998    0.050424143     2.02E-05
 Mm.4598       0.050424143     2.04E-05
 Mm.10728     0.101013086     4.89E-05
 Mm.162744   0.106930684     6.34E-05
 Mm.247564   0.106930684     6.91E-05
 Mm.269384   0.115716969     8.62E-05
 Mm.212428   0.115716969     9.34E-05
 Mm.457989   0.118548889     0.000126578
 Mm.154662   0.118548889     0.000128005
 Mm.21005     0.118548889     0.000133975
 Mm.5109       0.149489879     0.000196053
 Mm.207432   0.149489879     0.00020444

Does anyone know why several probesets have the same adjusted p value even
though the regular p value is different for each gene?  I'm 90% sure this is
just my ignorance about the BH method, but I'll be very thankful to anyone
who can point me in the right direction.  Thanks in advance,

Dave Young

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] limma_3.8.3              mouse430a2mmugcdf_14.1.0 simpleaffy_2.28.0
   gcrma_2.24.1
[5] genefilter_1.34.0        affy_1.30.0              Biobase_2.12.2


loaded via a namespace (and not attached):
 [1] affyio_1.20.0         annotate_1.30.1       AnnotationDbi_1.14.1
 Biostrings_2.20.3
 [5] DBI_0.2-5             IRanges_1.10.6        preprocessCore_1.14.0
RSQLite_0.9-4
 [9] splines_2.13.1        survival_2.36-9       tools_2.13.1
 xtable_1.5-6

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