[BioC] passing my data to siggenes package

Sean Davis sdavis2 at mail.nih.gov
Wed Oct 26 12:30:07 CEST 2005

On 10/26/05 3:45 AM, "madhurima bhattacharjee"
<madhurima_b at persistent.co.in> wrote:

> Hi All,
> I am using the siggenes package for SAM analysis.
> I have tried out the package with golub data from multtest package.
> But I cant understand how to pass my own expression data to the package.
> Can anyone plz help ASAP?

One way is to make a matrix from your data where rows represent genes and
columns represent samples.  Then, you need to make your class vector.  Some
examples are in the package vignette.  If you call your matrix "mymat" and
your class vector "my.cl", then you can simply replace "golub" with "mymat"
and "golub.cl" with "my.cl" and run the examples as given.  I think the gene
names are optional, but you can make your own vector of gene names to pass
to SAM, also, if you like.

I'm not sure what the particular hang-up is for you, so you will have to
send us more details and code of what you have tried and how it has failed
for anyone to help more.


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