[BioC] about gene annotation

[James W. MacDonald]

Hi Yanju,

yanju wrote:
> Hello all,
> 
> I was tring to annotate zelbrafish microarray data using genbank 
> function, but I got the following errors. Could you tell me what the 
> problem is?
> 
>     library(XML)
>     library(annotate)
>     genbank("AW116961")

You will have to give more information (as the posting guide suggests), 
namely the ouput from sessionInfo(). Anyway, this works OK for me.

 > library(XML)
 > library(annotate)
 > a <-  genbank("AW116961")
Read 402 items
Read 569 items
 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
annotate  Biobase      XML
"1.12.1" "1.12.2"  "1.4-0"

Best,

Jim



> 
> 
> Entity: line 47: parser error : Opening and ending tag mismatch: link 
> line 29 and head
>     </head>
>            ^
> Entity: line 67: parser error : EntityRef: expecting ';'
> ryBox" 
> action="http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi?CMD=search&DB
> ........
> ........
> 
>  *** caught segfault ***
> address 0xc0000000, cause 'memory not mapped'
> Segmentation fault
> 
> but if i show the result using browser like 
> genbank("AW116961",disp=c("browser")), it works fine.
> what is the problem???
> 
> Thanks in advance
> 
> Regards,
> Yanju
> 
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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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