Re: [R] Significance analysis of Microarrays (SAM)

From: Eleni Christodoulou <elenichri_at_gmail.com>
Date: Wed, 07 May 2008 11:02:03 +0300

Thanks Martin,

I also posted the question on the bioconductor list but I have no reply yet. In the meanwhile I found out that instead of saying d=list(data.matrix2,y,censored)

I should specify the arguments:
d=list(x=data.matrix2,y=y,censoring.status=censored)

Strange, huh? Anyway, it solves the problem.

Thanks once again,
Eleni

On Tue, May 6, 2008 at 6:43 PM, Martin Morgan <mtmorgan_at_fhcrc.org> wrote:

> Hi Eleni --
>
> Although samr is not a Bioconductor package, you might have more luck
> asking on the Bioconductor mailing list, http://bioconductor.org. The
> obvious place to start, and probably you have already done this, is to
> ensure that the class of the objects passed to the function agree with
> the classes described on the function help page.
>
> Martin
>
> "Eleni Christodoulou" <elenichri_at_gmail.com> writes:
>
> > Dear list,
> >
> > I am trying to perform a significance analysis of a microarray
> experiment
> > with survival data using the {samr} package. I have a matrix containing
> my
> > data which has 17816 rows corresponding to genes, and 286 columns
> > corresponding to samples. The name of this matrix is data.matrix2. Some
> of
> > the first values of this matrix are:
> > data.matrix2[1:3,1:5]
> > GSM36777 GSM36778 GSM36779 GSM36780 GSM36781
> > [1,] 1.009274 1.0740659 1.048540 1.015946 1.022650
> > [2,] 1.007992 0.8768410 0.962442 1.111742 1.121150
> > [3,] 0.981853 0.9606492 1.024987 1.053302 1.063408
> >
> > I also have the time in which each patient-sample is examined for
> relapse.
> > This information is in vector y, which has length 286, and is declared
> in
> > months. Indicatively:
> > y[1:5]
> > [1] 101 118 9 106 37
> >
> > Finally, I have a variable censored, which is 1 if the patient has
> relapsed
> > when examined at the examined time and 0 if not. Indicatively:
> > censored[1:5]
> > [1] 0 0 1 0 1
> >
> >
> > I am trying to perform the following sam analysis:
> > d=list(data.matrix2,y,censored)
> > samr.obj=samr(d,resp.type="Survival", nperms=20)
> >
> > When I am running the above commands I get the error:
> > Error in check.format(y, resp.type = resp.type, censoring.status =
> > censoring.status) :
> > Error in input response data: response type Survival specified;
> error in
> > censoring indicator
> > In addition: Warning message:
> > In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
> >
> >
> > I really cannot understand what is wrong with my code. Could anyone
> please
> > help me with this?
> >
> > Thank you all,
> > Eleni
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>

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