Hi!
Thanks for the response!
Regards,
Dhaarini.

On Wed, Mar 4, 2009 at 11:55 AM, dhaarini s <dhaarini87@gmail.com> 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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