[datatable-help] How to get only those values out of a matrix that are in a list

[Steve Lianoglou]

Hi Richelle,

As Matthew kindly pointed out -- you're knocking on the wrong dooR ;-)

Your question is really most appropriate to the bioconductor mailing
list, whose address you can find here (in the "mailing list" tile --
please see that posting guide, too ;-):

http://www.bioconductor.org/help/

Make sure you read through the help you can access for the topTable
function by running this in your R session:

R> library(limma)
R> ?topTable

Look at the "Value" section, as that is where the description of your
returned object is (look at `genelist` in particlar).

Lastly -- it will help if you read through "An Introduction to R" so
that you're familiar with basics of R programming (vectors,
data.frames, etc. and how to subset and index into them in
particular).

Good luck with your analysis!

-steve

On Tue, Jun 28, 2011 at 11:00 AM, Ingezz <irholtman at gmail.com> wrote:
> Hello everybody,
>
> I just started using R for my microarray analysis, so I am quite new to all
> of this. For now I have done preprocessing, normalization, limma and
> globaltest KEGG pathway analysis.
>
> I would like to see how each in gene in a certain pathway contributes the
> significance of the pathway. Therefore, I would like to combine the output
> of limma analysis and the genes that belong to a certain KEGG pathway.
> It is simple to get a list of genes that belong to a pathway in a vector,
> but I dont know how to pick only those genes from the limma toplist-file,
> with all the belonging statistics and make a new datamatrix from that. I
> hope my story is a bit clear, cause I dont know the exact R terminology.
>
> I have googled this, read many online introductions to R, but I cannot find
> it. I hope I havent posted this in the wrong place, but I hope that their is
> someone who can help me. Is there a function that is capable of picking only
> those elements from a datamatrix that correspond to the elements of a list?
> That's basically what the question comes down to.
>
> Many thanks!
>
> Regards
> Richelle
>
> --
> View this message in context: http://r.789695.n4.nabble.com/How-to-get-only-those-values-out-of-a-matrix-that-are-in-a-list-tp3630580p3630580.html
> Sent from the datatable-help mailing list archive at Nabble.com.
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact