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

[Martin Morgan]

On 01/25/2012 10:56 AM, Jung [guest] wrote:
>
> 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.

Hi Jung -- see the help pages for gage (?gage) to find out what 'expr' 
is supposed to be. See the help page for readExpData (?readExpData; also 
?read.delim) and check class(Micro_array_data). Are there any problems?

Martin

> 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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>
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