[BioC] annotating genes using KEGG

[Saroj K Mohapatra]

Hi Dhaarini:

If you post the output of sessionInfo(), it might help others to understand the problem.

I could get the pathway ids thus.

> library("hgu133a.db")
> mget(c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at"), hgu133aPATH)
$`1007_s_at`
[1] NA

$`1053_at`
[1] NA

$`117_at`
[1] NA

$`121_at`
[1] "05216"

$`1255_g_at`
[1] "04740"

> sessionInfo()
> sessionInfo()
R version 2.8.0 (2008-10-20) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] hgu133a.db_2.2.0    AnnotationDbi_1.2.2 RSQLite_0.7-0      
[4] DBI_0.2-4           Biobase_2.0.1 

Hope it helps.

Saroj

----- Original Message -----
From: "dhaarini s" <dhaarini87 at gmail.com>
To: bioconductor at stat.math.ethz.ch
Sent: Wednesday, March 4, 2009 1:25:43 AM GMT -05:00 US/Canada Eastern
Subject: [BioC] annotating genes using KEGG

Hi all!
I have a dataset done on Affymetrix chip hgu133a. I would like to annotate
it. I followed the method to connect to pathway , from the book
"Bioinformatics and Computational Biology Solutions using R and
Bioconductor". This I did using the "annaffy" package. I got the probe IDs
of a pre-normalized dataset. Then tried connecting it to the KEGG pathway.
This is what I did:

> probeids<-featureNames(eset)
> paths <- aafPathway(probeids, "hgu133a")

(eset is my expression set). In the book, the example is given for
"hgu95av2". But when I use "hgu133a", I get an error as follows:

Loading required package: hgu133a
Error in .aaf.raw(probeids, chip, "PATH") :
  Couldn't load data package hgu133a
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return
= TRUE,  :
  there is no package called 'hgu133a'

So, I tried using "hgu133acdf", because that was what I found in the R
library. But then, when I gave hgu133acdf, again I got an error as follows:

> paths <- aafPathway(probeids, "hgu133acdf")
Error: object "hgu133acdfPATH" not found
Error in mget(c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at",  :
  error in evaluating the argument 'envir' in selecting a method for
function 'mget'

 Is there any other method for pathway analysis for hgu133a chip?? Please
help me!!
Thanks in advance,
Regards,
S.Dhaarini.

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