Bioconductors,
    I am working on a RNA seq analysis project and am having trouble
publishing an HTML report for it.  I am unsure of how to make my DE genes
have the same ID as what publish() will accept when passing an argument to
'annotation'.
    I mapped the reads using tophat and passed the TAIR 10 gtf file to the
-G option.  When i counted my reads I used the summarizeOverlaps function
from GenomicRanges and again used this same file.  I called differential
expression in edgeR using the GLM methods.  So the rownames  of my DE table
are the AGI identifiers (AT#G#####).  I loaded the org.At.tair.db
annotations and passed it to HTMLReport in:

publish(DGELists[["Roots"]], myHTML, countTable = cpmMat, conditions =
group, annotation = "org.At.tair.db", pvaueCutoff = 0.01, lfc =2, n = 1000,
name = "RootsLRT")
Error: More than half of your IDs could not be mapped.
In addition: Warning message:
In .DGELRT.to.data.frame(object, ...) : NAs introduced by coercion

which makes sense, because publish() is looking for Entrez IDs (right?)

How do I proceed?

Thanks in advance!
-- 
Sam McInturf

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