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dhaarini s
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70
@dhaarini-s-3305
Last seen 10.2 years ago
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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