[BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files

Tue Jan 17 21:51:49 CET 2012

Hello Valerie,
Thanks for your help. I am sending you the data files(Micro_array_dataset.txt** & Gene_Set.txt) which i want to use for the analysis.
I need to know in which format the files should be saved (like http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
this site explains in great detail, what should be the format of the data files required for GSEA analysis (though i am not using GSEA analysis or these file types), same way i want to know in which format i should save the data files required for GAGE analysis so that the analysis is done properly)
Please tell me which information is missing from these files.
* Yes i know that "gse16873" is expression data and "kegg.gs" is a geneset but i want to use my own, these ones are provided by the author.
1) What i want to accomplish is: I want to do a basic gage analysis (as given in the R script file named "GAGE.r" and pdf file "gage.pdf") such as t-test, rank test, KS test etc.

2) I copied the begining code(to make sure that it loads all the files successfully) from R script file provided by the author (which is also attached as GAGE.r)  and made some changes to it and saved as my own script (also attached as Gage_run.r). I tried to load the data files (Micro_array_dataset.txt & Gene_Set.txt) and got these errors (shown in "R Console.txt" file).

3) I run the R script file (Gage_run.r) first to see that it loads all the input files successfully and then i can move ahead with the tests. The output is shown in "R Console.txt" file which shows the errors and warnings.

If you need more additional information. Please do tell me. I will be happy to provide that.
**an expression matrix with genes as rows and samples as columns.
Thanks,
Jung
________________________________
From: Valerie Obenchain [vobencha at fhcrc.org]
Sent: Tuesday, January 17, 2012 10:04 AM
To: Javerjung Sandhu
Cc: bioconductor at r-project.org; luo_weijun at yahoo.com
Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files

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 at fhcrc.org<mailto:vobencha at fhcrc.org>]
Sent: Monday, January 16, 2012 3:18 PM
To: Javerjung Sandhu
Cc: bioconductor at r-project.org<mailto:bioconductor at r-project.org>; luo_weijun at yahoo.com<mailto:luo_weijun at 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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