I am no expert on the vocabulary here, but this shows two ways of working
with the ChipDb package.  First we use some SQL to figure out what is in
there

> library(hugene10sttranscriptcluster.db)

> con = hugene10sttranscriptcluster_dbconn()  # do dbListTables(con) too

> dbGetQuery(con, "select * from probes limit 5")
  probe_id gene_id is_multiple
1  7892501    <NA>           0
2  7892502    <NA>           0
3  7892503    <NA>           0
4  7892504    <NA>           0
5  7892505    <NA>           0

> peek = dbGetQuery(con, "select * from probes where gene_id is not null
limit 5")

> peek
  probe_id   gene_id is_multiple
1  7896740     81099           0
2  7896742    346288           0
3  7896744     81399           0
4  7896754 100287934           0
5  7896756    157693           0

# so now we know that there is some attribute 'probe_id' that maps to
something
# called gene_id.  now let's use the select interface

> somekeys = peek[,1]

> select( hugene10sttranscriptcluster.db, keytype="PROBEID", keys=somekeys,
columns=c("SYMBOL", "ENTREZID"))
  PROBEID       SYMBOL  ENTREZID
1 7896740       OR4F17     81099
2 7896742       SEPT14    346288
3 7896744       OR4F16     81399
4 7896754 LOC100287934 100287934
5 7896756       FAM87A    157693


> sessionInfo()
R Under development (unstable) (2013-12-01 r64371)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

locale:
[1]
en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

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

other attached packages:
 [1] hugene10sttranscriptcluster.db_8.0.1 org.Hs.eg.db_2.10.1

 [3] RSQLite_0.11.4                       DBI_0.2-7

 [5] AnnotationDbi_1.25.9                 Biobase_2.23.3

 [7] BiocGenerics_0.9.3                   BiocInstaller_1.13.3

 [9] weaver_1.29.1                        codetools_0.2-8

[11] digest_0.6.4

loaded via a namespace (and not attached):
[1] IRanges_1.21.21 stats4_3.1.0



On Tue, Jan 28, 2014 at 4:18 AM, Stephane Plaisance | VIB | <
stephane.plaisance@vib.be> wrote:

> I am looking for a file or package that can map my transcript_cluster_id
> to hgnc symbols (human)
> my data was preprocessed using APT and I do not have the original probe
> IDs.
>
> Apparently, only 'probeIDs' are supported by BiomaRt, not
> 'transcript_cluster_id'.
> I tried hugene10sttranscriptcluster.db" but the IDs are different
> (probeIDs)
>
> Where can I find a table listing 'transcript_cluster_id' and enough info
> to get symbols?
>
> thanks in advance
> Stephane
>
>
>
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>
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