after you obtain credentials from netaffx, you can do something like the
following

library(AffyCompatible)
rsrc = NetAffxResource(user=[user], password=[pass])
lk = grep("Ex", names(rsrc), value=TRUE)
names(rsrc[[lk[3]]])
fl = readAnnotation(rsrc, anno=rsrc[["HuEx-1_0-st-v2", "Transcript Cluster
Annotations, CSV"]], content=FALSE)
con = unz(fl, "HuEx-1_0-st-v2.na33.1.hg19.transcript.csv")
smal = read.csv(con, skip=24, nrow=20, stringsAsFactors=FALSE)  # drop the
nrow for full     # import
smal[,1:7]

> smal[,1:7]
   transcript_cluster_id probeset_id seqname strand  start   stop
total_probes
1                2315100     2315100    chr1      +  11884  14409
20
2                2315106     2315106    chr1      +  14760  15198
 8
3                2315109     2315109    chr1      +  19408  19712
 4
4                2315113     2315113    chr1      +  27563  27813
 4
5                2315115     2315115    chr1      +  28425  29158
 4
6                2315117     2315117    chr1      +  30623  30667
 4
7                2315119     2315119    chr1      +  35690  35804
 4
8                2315121     2315121    chr1      +  35928  35968
 2
9                2315125     2315125    chr1      +  51913  70633
26
10               2315129     2315129    chr1      +  52452  63887
20
11               2315145     2315145    chr1      + 115060 116054
 4
12               2315147     2315147    chr1      + 131158 146731
44
13               2315160     2315160    chr1      + 136242 136557
 8
14               2315163     2315163    chr1      + 138440 662350
85
15               2315189     2315189    chr1      + 140341 140737
 4
16               2315191     2315191    chr1      + 141298 320283
15
17               2315198     2315198    chr1      + 148041 682717
20
18               2315206     2315206    chr1      + 158150 164721
 8
19               2315209     2315209    chr1      + 236570 238386
 8
20               2315212     2315212    chr1      + 237097 237462
 4

substr(smal[,8], 1, 60)

> substr(smal[,8], 1, 60)
 [1] "NR_046018 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box hel"
 [2] "AK092583 // WASH7P // WAS protein family homolog 7 pseudogen"
 [3] "NR_033266 // WASH5P // WAS protein family homolog 5 pseudoge"
 [4] "---"
 [5] "ENST00000422679 // MIR1302-11 // microRNA 1302-11 // --- // "
 [6] "ENST00000473358 // MIR1302-11 // microRNA 1302-11 // --- // "
 [7] "NR_026818 // FAM138A // family with sequence similarity 138,"
 [8] "ENST00000448235 // FAM138F // family with sequence similarit"
 [9] "NM_001005240 // OR4F17 // olfactory receptor, family 4, subf"
[10] "ENST00000492842 // OR4G11P // olfactory receptor, family 4, "
[11] "---"
[12] "ENST00000432723 // CICP7 // capicua homolog (Drosophila) pse"
[13] "AK303004 // FLJ45445 // uncharacterized LOC399844 // 19p13.3"
[14] "AK302487 // FLJ45340 // uncharacterized LOC402483 // 7q32.1 "
[15] "NR_039983 // LOC729737 // uncharacterized LOC729737 // 1p36."
[16] "ENST00000570230 // LOC100653348 // uncharacterized LOC100653"
[17] "NR_039983 // LOC729737 // uncharacterized LOC729737 // 1p36."
[18] "NR_029401 // LOC731275 // uncharacterized LOC731275 // 1q43 "
[19] "ENST00000424587 // LOC100508047 // uncharacterized LOC100508"
[20] "NR_029406 // FLJ43681 // ribosomal protein L23a pseudogene /"

so it appears you have to parse the 8th column to get the symbols






On Tue, Jan 28, 2014 at 5:11 AM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:

> for the record, my reply goes down the wrong path, to gene 1.0 st
> annotation.
>
> it seems likely that the solution lies in AffyCompatible package, and that
> resource should
> be mentioned in
>
> http://www.bioconductor.org/help/workflows/arrays/
>
>
> On Tue, Jan 28, 2014 at 4:41 AM, Vincent Carey <stvjc@channing.harvard.edu
> > wrote:
>
>> 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
>>>
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>

	[[alternative HTML version deleted]]

