Dear list, For the GAGE analysis, i am getting an error shown below. Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I got the gene sets, expression data and reference and target files ready for it and it seems that files are in proper format and i am also reading them in proper way but still the GAGE shows an error. Could anybody help me? I have saved the output from R command session (attached as text file) which also contains the header info for the files used in the analysis Script file shown below: #!/usr/bin/env Rscript library(gage) options(width=80) Micro_array_data <- readExpData(file = "geo30195_expression_data_19_Jan_2012.gct", row.names = 1) Gene_set <- readList("c1.all.v3.0.symbols.gmt") Phenotype <- read.table(file = "geo30195_phenotype_19_Jan_2012_RAEB_vs_RA.cls", header = TRUE, sep = "\t", quote = "") Col_names <- colnames(Phenotype) Reference <- grep("RAEB",Col_names,ignore.case = F) Target <- grep("ra",Col_names,ignore.case = F) gstTest <- gage(exprs = Micro_array_data, gsets = Gene_set, ref = Reference, samp = Target, set.size = c(1,1000), same.dir = FALSE, compare = "as.group", rank.test = TRUE, saaTest = gs.tTest) # Samples of all the data files used head(Micro_array_data) head(Gene_set) head(Phenotype) print(Reference) print(Target) Cheers, Jung -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: R console.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20120224="" 7e04f1ab="" attachment.txt="">

________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Javerjung Sandhu [jsandhu@bcgsc.ca] Sent: Friday, February 24, 2012 4:03 PM To: bioconductor at r-project.org Cc: luo_weijun at yahoo.com Subject: [BioC] Error in GAGE analysis, help URGENTLY required Dear list, For the GAGE analysis, i am getting an error shown below. Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I got the gene sets, expression data and reference and target files ready for it and it seems that files are in proper format and i am also reading them in proper way but still the GAGE shows an error. Could anybody help me? I have saved the output from R command session (attached as text file) which also contains the header info for the files used in the analysis Script file shown below: #!/usr/bin/env Rscript library(gage) options(width=80) Micro_array_data <- readExpData(file = "geo30195_expression_data_19_Jan_2012.gct", row.names = 1) Gene_set <- readList("c1.all.v3.0.symbols.gmt") Phenotype <- read.table(file = "geo30195_phenotype_19_Jan_2012_RAEB_vs_RA.cls", header = TRUE, sep = "\t", quote = "") Col_names <- colnames(Phenotype) Reference <- grep("RAEB",Col_names,ignore.case = F) Target <- grep("ra",Col_names,ignore.case = F) gstTest <- gage(exprs = Micro_array_data, gsets = Gene_set, ref = Reference, samp = Target, set.size = c(1,1000), same.dir = FALSE, compare = "as.group", rank.test = TRUE, saaTest = gs.tTest) # Samples of all the data files used head(Micro_array_data) head(Gene_set) head(Phenotype) print(Reference) print(Target) Cheers, Jung -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: R console.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20120227="" b65ee862="" attachment.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00001.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20120227="" b65ee862="" attachment-0001.txt="">