[BioC] URGENT Help required: Getting this error with GAGE analysis

[Jung [guest]]

Hi there,
I am getting this error on R console. The format of the input files, Micro_array_dataset.txt and Gene_set.gmt is shown below:
Micro_array_dataset.txt sample shown below, it's a tab delimited file:
Gene	TCGA_AB_2803	TCGA_AB_2805	TCGA_AB_2806	TCGA_AB_2807	TCGA_AB_2808	TCGA_AB_2810
TSPAN6	0.87040619	0	0	1.49516441	0.145067698	0
TNMD	0.14858841	0.037147103	0	0	0	0
DPM1	45.07516892	63.28462838	64.9535473	41.44256757	46.61233108	42.66807432
SCYL3	12.62339374	22.15584843	25.60428336	13.98088962	17.0583196	4.036902801

Gene_set.gmt is a Gene Matrix Transposed file format required for GSEA analysis, sample shown below:
chr5q23	na	PTMAP2	FTMT	PRR16	MGC32805
chr16q24	na	LOC642452	SNORD68	RPL13	TRAPPC2L
chr8q24	na	LYPD2	KIFC2	EIF2C2	ADCY8
chr13q11	na	LOC645626	ZMYM2	FGF9	XPO4
chr7p21	na	DNAH11	LOC221814	MYL7	CRS


Any kind of help to get rid of the error shown below will  be really appreciated.
Thanks,

Jung



 -- output of sessionInfo(): 

> Micro_array_data <- readExpData(file = "Micro_array_dataset.txt")
> Gene_set <- readList("Gene_set.gmt")
> Reference_condition <- c(1,3,5)
> Target_condition <- c(2,4,6)
> A1_compare_un <- gage(Micro_array_data, Gene_set, ref = Reference_condition, samp = Target_condition)
Error in saaPrep(exprs, ref = ref, samp = samp, same.dir = same.dir, compare = compare,  : 
  exprs needs to be a numeric matrix or vector
> # Essential_member_genes <- essGene(Gene_set, Micro_array_data,ref = NULL)
> # Non_redundant_significant_gene_set_list <- esset.grp()
>

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