I asked a similar question yesterday - wanted to clarify and give more
information. I am using limma to analyze microarray data from Affymetrix
HuGene 1.0 ST arrays. I'm reading in the CEL files using ReadAffy. Both
sources of annotation confirm that I'm using the hugene1.0st array:

> affybatch@cdfName
[1] "HuGene-1_0-st-v1"
> eset@annotation
[1] "hugene10stv1"

I fit a model, and now I want to annotate the results with gene symbols
rather than the probeset IDs:

> fit <- lmFit(eset, design)
> head(fit$genes)
       ID
1 7892501
2 7892502
3 7892503
4 7892504
5 7892505
6 7892506

When I try to use getSYMBOL (as per Gordon's suggestion from a previous
post:https://stat.ethz.ch/pipermail/bioconductor/2011-February/037866.html),
none of these symbols map:

> getSYMBOL(head(fit$genes$ID), "hugene10stprobeset.db")
7892501 7892502 7892503 7892504 7892505 7892506
     NA      NA      NA      NA      NA      NA

In fact, of my 32,321 probeset IDs, only 150 match up with the IDs in the
hugene10stprobeset.db package:
> mapped_probes <- mappedkeys(hugene10stprobesetSYMBOL)
> head(mapped_probes)
[1] "7896741" "7896743" "7896745" "7896755" "7896757" "7896758"
> length(fit$genes$ID)
[1] 32321
> length(mapped_probes)
[1] 238111
> sum(fit$genes$ID %in% mapped_probes)
[1] 150

Thanks in advance for any help!

Stephen

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

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

other attached packages:
 [1] hugene10stv1probe_2.9.0     BiocInstaller_1.2.1
hugene10stv1cdf_2.9.1       hugene10stprobeset.db_8.0.1
 [5] org.Hs.eg.db_2.6.4          RSQLite_0.11.1              DBI_0.2-5
              annotate_1.32.1
 [9] AnnotationDbi_1.16.10       pvclust_1.2-2               calibrate_1.7
              gplots_2.10.1
[13] KernSmooth_2.23-7           caTools_1.12                bitops_1.0-4.1
             gdata_2.8.2
[17] gtools_2.6.2                limma_3.10.1
 arrayQualityMetrics_3.10.0  affy_1.32.0
[21] Biobase_2.14.0

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