[BioC] globaltest - multinomial model

[J.J.Goeman at lumc.nl]

 Dear Hans-Ulrich,

This is a minor bug, which has, I believe, been fixed in the latest
devel version. The worst thing that can happen is that you miss a
warning that the null model did not converge before the maximum number
of iterations.

If you want you can check this by asking for

fit(gt)@iter

after gt <- globaltest(Golub, "Source")

If this is smaller than 20 the null model has converged.

Regards,

Jelle


 

> -----Original Message-----
> From: Hans-Ulrich Klein [mailto:h.klein at uni-muenster.de] 
> Sent: 16 August 2007 19:31
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] globaltest - multinomial model
> 
> Hi List,
> 
> I get a warning message whenever I use the function globaltest with a 
> multinomial model. Below is a code example taken from the vignette 
> leading to the warning message:
> Warning message:
> $ operator not defined for this S4 class, returning NULL in: fit$iter
> 
> Should I be concerned about the warning message?
> 
> Regards,
> Hans-Ulrich
> 
> 
> 
>  > library(globaltest)
>  > library(golubEsets)
>  > library(vsn)
>  > data(Golub_Merge)
>  > Golub <- Golub_Merge[, 1:34]
>  > exprs(Golub) <- exprs(vsn2(Golub_Merge[, 1:34]))
> 
>  > globaltest(Golub, "Source")
> Global Test result:
> Data: 34 samples with 7129 genes; 1 gene set
> Model: multinomial
> Method: Asymptotic distribution
> 
>     Genes Tested Statistic Q Expected Q sd of Q    P-value
> all  7129   7129      23.126         10  1.9632 2.5091e-05
> Warning message:
> $ operator not defined for this S4 class, returning NULL in: fit$iter
> 
> 
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
> 
> locale:
> C
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  
> "grDevices" "utils"   
> [7] "datasets"  "methods"   "base"    
> 
> other attached packages:
>        vsn      limma       affy     affyio golubEsets globaltest   
> multtest
>    "2.2.0"   "2.10.0"   "1.14.2"    "1.4.1"    "1.4.3"    "4.6.0"   
> "1.16.1"
>   survival    Biobase
>     "2.32"   "1.14.1"
> 
> 
>