[BioC] agi4x44kpreprocess: `GEhelp` and `Treatment` variables

[James W. MacDonald]

Hi Stephen,

First, please don't take conversations off-list. We like to think of 
the archives as a searchable repository, and if conversations go 
private then that usefulness is diminished.

On Friday, November 15, 2013 1:02:28 PM, Stephen Hwang wrote:
> Mr. MacDonald,
>
> I appreciate the response. The reason why I was so drawn to the
> Agi4x44Preprocess was because it automatically generates files for
> GSEA (Broad Institute's application). My goal is to pipeline
> everything through R so there is no need for manual inputs into the
> application. Do you have any experience in preparing this data?

If you want to pipeline everything through R, then why are you trying 
to prepare data to use outside of R? There are any number of ways to 
perform GSEA type analyses from within R. You could use for instance 
the GSEABase package with GSEAlm or Category, or you could do 
substantively similar things using limma, with the romer or roast or 
camera functions, all of which can be easily added to your pipeline.

I don't personally have any experience preparing data for the Broad's 
application, so I can't be of much help other than pointing out that 
you can always grab the code for gsea.files and modify it to suit your 
input data.

Best,

Jim


>
> --
> Stephen Hwang
> MS, Bioinformatics
> Advanced Academic Program
> Johns Hopkins University
>
>
> On Wed, Nov 13, 2013 at 4:24 PM, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Stephen,
>
>
>     On Wednesday, November 13, 2013 2:16:50 PM, Stephen Hwang wrote:
>
>         I recently came across your R package `Agi4x44PreProcess` and
>         I'm having
>         issues with the filtering step due to my `targets` file (I did
>         not include
>         a `Treatment` or a GErep` column).
>
>                         Cy3              Cy5
>         Array1:  pre-drug    pre-drug
>         Array2:  pre-drug    post-drug
>         Array3:  post-drug  pre-drug
>
>         How would I label these groups? If treatment groups are 'pre-pre',
>         'pre-post', and 'post-pre', are the GErep values would be `1`,
>         `2`, and
>         `3`, corresponding to each treatment group?
>
>
>     The Agi4x44PreProcess package is designed for Agilent 4x44 arrays,
>     which if I am not mistaken are all single channel arrays. It
>     appears you are not using that type of array, so you would likely
>     be better served by using the limma package directly.
>
>     There are numerous examples in the limma User's Guide that show
>     how to analyze two channel arrays:
>
>     http://www.bioconductor.org/__packages/release/bioc/__vignettes/limma/inst/doc/__usersguide.pdf
>     <http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf>
>
>     Best,
>
>     Jim
>
>
>
>
>                 [[alternative HTML version deleted]]
>
>         _________________________________________________
>         Bioconductor mailing list
>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>         https://stat.ethz.ch/mailman/__listinfo/bioconductor
>         <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>         Search the archives:
>         http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>         <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>
>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>
>
>
> --
> Stephen Hwang
> MS, Bioinformatics
> Advanced Academic Program
> Johns Hopkins University

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099