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. [[alternative HTML version deleted]]

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. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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@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. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology VBI @ Virginia Tech

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. > > > > > [[alternative HTML version deleted]]