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

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Tue, 06 May 2008 08:43:00 -0700

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]]
>
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-- 
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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Received on Tue 06 May 2008 - 16:16:27 GMT

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