BUGRe: [BioC] Error message from running SAM for one-class case(siggenes)

[Fangxin Hong]

I check the source code, I found a bug in function xy.cal, line 19

x<-rep(1,length(cl))
should be
x<-which(cl==1)

Any idea? I think that is the reason.

Fangxin

> Hi there:
> I tried to run SAM for one-class case , using package siggenes.
> (R 1.9.1, siggenes Version: 1.0.6)
>
> My data set contains 2000 genes with 4 replications. I got the following
> error message:
> --------------------------
> Warning: There are 2000 genes which have variance Zero or no non-missing
> values.
>          The d-value of these genes is set to NA.
>
> Error in var(v) : missing observations in cov/cor
> --------------------------------
> I checked siggenes vignette, they didn't out down any example for
> one-class study. I tried to use the data(golub)(used as example in the
> vignette)  to do one-sample case as following
> -------------------------------------
>> temp=sam(golub[,1:10],golub.cl[1:10],rand=123)
> SAM Analysis for the one-class case.
>
> Warning: Expected classlabel is 1. cl will thus be set to 1.
>
> Warning: There are 1041 genes which have variance Zero or no non-missing
> values.
>          The d-value of these genes is set to NA.
>
> Error in var(v) : missing observations in cov/cor
> ----------------------------
> Although this is not an appropriate data set for one-class study, but SAM
> should still work. Anybody has idea about this, I would appreciate for any
> hint.
> BTW, I used Excel SAM program before, it was OK for this kind one-class
> study.
>
> Thank you all!
> Fangxin
>
>
>
>
> --
> Fangxin Hong, Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
>
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>


-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu