[BioC] annotating genes using KEGG

[James W. MacDonald]

Hi Dhaarini,

You need to install a package before you can use it. The error message 
there is no package called 'hgu133a' is supposed to indicate to you that 
the package isn't installed.

In addition, the package you want is now called hgu133a.db, so you want

source("http://www.bioconductor.org/biocLite.R")
biocLite("hgu133a.db")
paths <- aafPathway(probeids, "hgu133a.db")

Best,

Jim




dhaarini s wrote:
> 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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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826