[R-sig-ME] lmer in R-devel suddenly failing using code that worked just a few days ago

Mark W Kimpel mwkimpel at gmail.com
Thu Mar 20 18:57:12 CET 2008

lmer is producing an error using code that was working for me just a few 
days ago. Output and sessionInfo() follows. Note that the warning 
message has always been present. Thanks, Mark

 >           Treatment <- factor(pData(AOP$eSet)$Treatment)
 >           Tissue <- factor(pData(AOP$eSet)$Tissue)
 >           Rat <- factor(pData(AOP$eSet)$Rat)
 >           Tissue <- factor(pData(AOP$eSet)$Tissue)
 >           mod1 <- lmer(gene.mat[1,] ~  Treatment + Tissue + (1|Rat))
Warning message:
In .local(x, ..., value) :
   Estimated variance for factor ‘Rat’ is effectively zero

 > mod1
Error in printMer(object) :
   no slot of name "status" for this object of class "table"

Enter a frame number, or 0 to exit

1: function (object)
2: function (object)
3: printMer(object)

Selection: c
Enter an item from the menu, or 0 to exit
Selection: 0
 > sessionInfo()
R version 2.7.0 Under development (unstable) (2008-03-05 r44683)


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

other attached packages:
  [1] lme4_0.99875-9       Matrix_0.999375-5    lattice_0.17-6
  [4] affycoretools_1.11.4 annaffy_1.11.5       KEGG.db_2.1.3
  [7] gcrma_2.11.4         matchprobes_1.11.1   biomaRt_1.13.9
[10] RCurl_0.8-3          GOstats_2.5.2        Category_2.5.7
[13] genefilter_1.17.12   survival_2.34        RBGL_1.15.7
[16] annotate_1.17.11     xtable_1.5-2         GO.db_2.1.3
[19] AnnotationDbi_1.1.26 RSQLite_0.6-8        DBI_0.2-4
[22] graph_1.17.17        limma_2.13.6         affy_1.17.9
[25] preprocessCore_1.1.5 affyio_1.7.17        Biobase_1.99.3

loaded via a namespace (and not attached):
[1] cluster_1.11.10 grid_2.7.0      XML_1.93-2

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)


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