[BioC] limma warning: Estimation of var.prior failed

Georg Otto georg.otto at tuebingen.mpg.de
Thu Aug 14 21:00:11 CEST 2008


I am processing a set of around 40 Affymetrix hybridizations of (I
think) quit good quality. When I run limma on the rma-normalized set,
everything runs smoothly.

> fit<-lmFit(eset.rma, design)
> fit<-eBayes(fit)

However when I do the same thing on the gcrma-normalized set, I
receive a warning:

> fit<-lmFit(eset.gcrma, design)
> fit<-eBayes(fit)
Warning message:
In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) :
  Estimation of var.prior failed - set to default value

Could somebody explain me, what this possibly means and if this might
affect the results in any adverse way? Any help will be appreciated.



> sessionInfo()
R version 2.7.1 (2008-06-23) 


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] affycoretools_1.12.0 annaffy_1.12.1       KEGG.db_2.2.0       
 [4] gcrma_2.12.1         matchprobes_1.12.0   biomaRt_1.14.0      
 [7] RCurl_0.9-3          GOstats_2.7.0        Category_2.6.0      
[10] genefilter_1.20.0    survival_2.34-1      RBGL_1.16.0         
[13] annotate_1.18.0      xtable_1.5-2         GO.db_2.2.2         
[16] AnnotationDbi_1.3.8  RSQLite_0.6-9        DBI_0.2-4           
[19] graph_1.18.1         affy_1.18.2          preprocessCore_1.2.0
[22] affyio_1.8.0         Biobase_2.0.1        limma_2.14.5        

loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.95-2

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