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Question: Help with GSEA package
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gravatar for Jillian Rowe
8.0 years ago by
Jillian Rowe20
Jillian Rowe20 wrote:
Hello all, I am very new to R, and am confused with the GSEA package. I am running an analysis on a group of CEL files from two treatment groups. (I'm sorry this is so long. I just wanted to make sure there were lots of comments and no block o' text) # loads all required libraries for this assignment source(" http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/cluste rIndex.R<http: faculty.ucr.edu="" %7etgirke="" documents="" r_biocond="" my_r_scr="" ipts="" clusterindex.r=""> ") source(" http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/my.col orFct.R<http: faculty.ucr.edu="" %7etgirke="" documents="" r_biocond="" my_r_scri="" pts="" my.colorfct.r=""> ") source(" http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/dendro Col.R<http: faculty.ucr.edu="" %7etgirke="" documents="" r_biocond="" my_r_script="" s="" dendrocol.r=""> ") ## Libraries library( hu6800cdf ) library( hu6800.db ) library( affy ) library( genefilter ) library( multtest ) library( siggenes ) library( annaffy ) library(affyPLM) library(multtest) library(cluster) library(pvclust) library(gplots) library(ALL) library(hgu95av2.db) library(KEGG.db) library(GSEABase) library(affyPLM) library(GO.db) #set the working directory to ensure R is pointing to correct directiy to read the CEL files setwd("/home/jill/Desktop/Microarray/Assignments/CEL") #read the CEL files separated by semicolon with hearder into #pd by read.annotated dataframe method pd <- read.AnnotatedDataFrame( "treat.txt", header=T, row.names=1, sep=";" ) # verify to see how your phonodata ( sample information ) pData(pd) ##Diabetic ##GSM391693.CEL a ##GSM391694.CEL a ##GSM391695.CEL a ##GSM391696.CEL a ##GSM391697.CEL a ##GSM391702.CEL b ##GSM391703.CEL b ##GSM391704.CEL b ##GSM391705.CEL b ##GSM391706.CEL b # read the files using ReadAffy # if you do not supply any argument , it will read all CEL files from your working directory expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) # QC library(affyPLM); dataPLM = fitPLM(expression_data); pdf("nuse_plot.pdf"); boxplot(dataPLM, main="NUSE", ylim=c(0.95,1.1), outline= FALSE, col="lightblue", las=3, whisklty = 0 , staplelty = 0); dev.off() ##pdf 2 # performs GCRMA background correct ,normalization and summarization esetGCrma <- justRMA(filenames=rownames(pData(pd))) # removes genes from the RMA normalized sets with an IQR greater than 0.5 selector<-function(x) (IQR(x)> 0.5); a1 <- filterfun(selector); gcrma_filtered<- genefilter(esetGCrma, a1); sum(gcrma_filtered); ##[1] 2985 gcrma_data_selected <- esetGCrma[gcrma_filtered,]; cl <-as.numeric(pd$Diabetic=="a"); # nonspecific filter: remove genes that does not ## show much variation across samples #Load KEGG and GSEABase package. #Do a GeneSetCollection for KEGG. #Construct an incidence matrix. ####End of working code! Now, what I think I should do is: gsc <- GeneSetCollection(gcrma_data_selected, setType=KEGGCollection()) But I get this error: Error in as.list(getAnnMap("PATH2PROBE", annotation(idType))) : error in evaluating the argument 'x' in selecting a method for function 'as.list' I have some sample data that uses data from the ALL library, and it inputs a data object from the genefilter function as well. Any help would be very, very appreciated. Thanks! Jillian [[alternative HTML version deleted]]
ADD COMMENTlink modified 8.0 years ago by Martin Morgan ♦♦ 22k • written 8.0 years ago by Jillian Rowe20
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gravatar for Martin Morgan
8.0 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
Hi Jillian -- On 12/02/2010 06:27 AM, Jillian Rowe wrote: > Hello all, > > I am very new to R, and am confused with the GSEA package. > > I am running an analysis on a group of CEL files from two treatment groups. All that code was bit intimidating! > But I get this error: > > Error in as.list(getAnnMap("PATH2PROBE", annotation(idType))) : > error in evaluating the argument 'x' in selecting a method for function > 'as.list' Unpack this a little. You're making a call to getAnnMap inside as.list. What does getAnnMap return? I'd bet it throws an error getAnnMap("PATH2PROBE", annotation(idType)) and then unpack that and see how the argument annotation(idType) compares to the documentation ?getAnnMap. Perhaps you meant annotation(gcrma_data_selected), but its hard to tell -- simplify the code you present; in the process it might shed light on what the underlying problem is. Hope that helps! Martin > > I have some sample data that uses data from the ALL library, and it inputs a > data object from the genefilter function as well. > > Any help would be very, very appreciated. > > Thanks! > > Jillian > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 8.0 years ago by Martin Morgan ♦♦ 22k
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