[BioC] hs133phsentrezg metadata

[James W. MacDonald]

De Bondt, An-7114 [PRDBE] wrote:
> Dear useR,
> 
> The 'hs133phsentrezg' metadata have only 'hs133phsentrezgGENENAME' mapping
> info.  The 'hgu133plus2' metadata has also 'hgu133plus2CHRLOC' info (besides
> lots of other info).  How can I find 'hs133phsentrezgCHRLOC' info?

I hadn't realized how sparse the information in these annotation 
packages really is. I think your best bet is to use biomaRt to get the 
annotation you want.

Something like

 > mart <- useMart("ensembl","hsapiens_gene_ensembl")
Checking attributes and filters ... ok
 > a <- getBM("chromosome_location", "entrezgene", sub("_at", "", 
ls(hs133phsentrezgGENENAME)[1:10]), mart=mart, output="list")
 > sapply(a[[1]], length)
     1    10   100  1000 10000 10001 10002 10003 10004 10005
    62   157   233  1457   907   105    92   371    80   123
 > a[[1]][[1]]
  [1] 63544227 63545175 63546378 63546412 63547557
  [6] 63547599 63547672 63548610 63548624 63548943
[11] 63549372 63549373 63549374 63549543 63550044
[16] 63550148 63556679 63556692 63556702 63556866
[21] 63556880 63556894 63556903 63557399 63557422
[26] 63557669 63558246 63558375 63559327 63559846
[31] 63560064 63560292 63560992 63561327 63561328
[36] 63561647 63561650 63550747 63553556 63556291
[41] 63556303 63550430 63550488 63550864 63550878
[46] 63551634 63552081 63552199 63552253 63552624
[51] 63552827 63553507 63554072 63554973 63554974
[56] 63554975 63554981 63554982 63554984 63555253
[61] 63555261 63555962

Should do the trick.

HTH,

Jim


> 
> Thanks in advance,
> An De Bondt
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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