Hello,

I think the vignette is clear that you need (1) a gene set and (2) a 
mircoarray dataset to run the gage analysis.  On page 4 they mention the 
importance of having the same ID system for your gene set and expression 
data. Once this is accomplished you can use the gage() function.

## this is the expression data
gse16873

## this is the gene set
kegg.gs

## call to gage() using 'HN' as control and 'DCIS' as treatment
gse16873.kegg.p <- gage(gse16873, gsets = kegg.gs,
     ref = hn, samp = dcis)


I belive if you have only one column of expression data the 'ref' and 
'samp' arguments should be omitted (i.e., default of NULL). Read ?gage 
for details. Maybe the package author will comment on this. I've cc'd 
them on this message.

It is still not clear to me what you have tried. It would be helpful to 
know the following,

(1) what is your analysis question (what are you trying to accomplish)
(2) what have you tried (what functions have you used)
(3) what errors have you seen from #2


Valerie









On 01/16/2012 04:19 PM, Javerjung Sandhu wrote:
> Hi Valerie,
> First of all thanks a lot for replying and helping me. I really appreciate that. I am sending you the R source code file which the GAGE analysis uses plus two other documents which explains what that package does.
> These are the data files used by the GAGE analysis:
> ----------------------------
> Data sets in package ‘gage’:
> carta.gs               Common gene set data collections
> egSymb                 Mapping between Entrez Gene IDs and official
>                         symbols
> go.gs                  Common gene set data collections
> gse16873               GSE16873: a breast cancer microarray dataset
> kegg.gs                Common gene set data collections
> -----------------------------------------------------
> I have only ONE tab delimited data file in the form of a MATRIX giving the gene expressions for 173 patients(as columns) and names of genes(as rows).
> I want to know how can i use this package and my data to do the GAGE analysis.
> If you need more information, please tell me. I will be ready to provide that.
> Thanks,
> Jung
>
> ________________________________________
> From: Valerie Obenchain [vobencha@fhcrc.org]
> Sent: Monday, January 16, 2012 3:18 PM
> To: Javerjung Sandhu
> Cc: bioconductor@r-project.org; luo_weijun@yahoo.com
> Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
>
> Hi Jung,
>
> Please provide the code you've tried and the error you are seeing. For
> example, did you read your own data into R, then try to use gage() and
> got an error? We can better help you if we understand your inputs and
> the function you're having trouble with.
>
> Valerie
>
>
> On 01/13/12 13:10, Javerjung Sandhu wrote:
>> Dear List,
>> I will highly appreciate your help on this.
>> For the GAGE analysis package shown by the link given below:
>> http://www.bioconductor.org/packages/release/bioc/html/gage.html
>> Could you please tell me how to prepare the Custom INPUT files required for this analysis
>> OR
>> Send me the SAMPLE DATA files in TXT format so that i know in which format i need to put the data&   how could i DO a BASIC  GAGE analysis using those files. I couldn't figure it out and trying it since 3 weeks or more.
>> Best Regards,
>> Jung
>>
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>>
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