[BioC] list of significant genes (siggenes)

Seth Falcon sfalcon at fhcrc.org
Fri Oct 28 17:02:29 CEST 2005

On 28 Oct 2005, Assa.Yeroslaviz at uni-duesseldorf.de wrote:

> Hi,
> i need some helpediting my resluts.
> I have a data frame( matrix ), 

data.frame is not the same as a matrix in R.  Have a look at the R
Intro manual for an overview, or read the man pages for ?data.frame
and ?matrix.

> whereas on the first column are the
> names of my items. Then I have a second object. This is the output
> of the line:
>> list.siggenes(data.out, delta)
> "item_1! "item_2" "item_3" "item_4" ...
> 1. Is this object is a vector or  just a list?

Ask R: 

  class(list.siggenes(data.out, delta))

> 2. How can i change this object to a matrix?

  Not enough info at this stage to help, I'm afraid.

> my second problem is in comparing both of the data. I want to
> compare the data frame with the list from 'list.siggenes' and to cut
> out all the line, which don't appear in both objects.

If you have a column (which would be a vector) that acts as the
primary key, you can use the intersect() function to find all ids that
appear in both.

+ seth

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