[BioC] FW: Error in GAGE analysis, help URGENTLY required

[Javerjung Sandhu]

________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Javerjung Sandhu [jsandhu at 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
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