[BioC] DESeq: Error: attempt to apply non-function

[Wolfgang Huber]

Dear João

can you (perhaps privately, or on a public filesharing place) make 
available to objects 'c' and 'group' so we can test this?

	Best wishes
	Wolfgang


João Barbosa scripsit 05/18/2011 05:16 PM:
> Hi,
>
> Does anyone suspect why I'm getting this error?
>
> Thanks,
>
>
>> dim(c)
> [1] 7065   16
>> group
>   [1] "isowt" "isowt" "isowt" "isowt" "rlp"   "rlp"   "rlp"   "rlp"   "ssr"
> [10] "ssr"   "ssr"   "ssr"   "xrlp"  "xrlp"  "xrlp"  "xrlp"
>
>> cds<- newCountDataSet( c, group)
>> cds<- estimateSizeFactors( cds )
>> cds<- estimateVarianceFunctions( cds )
> Error: attempt to apply non-function
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] DESeq_1.4.0           locfit_1.5-6          lattice_0.19-23
>   [4] akima_0.5-4           org.Sc.sgd.db_2.5.0   org.EcK12.eg.db_2.5.0
>   [7] RSQLite_0.9-4         DBI_0.2-5             genefilter_1.34.0
> [10] annotate_1.30.0       AnnotationDbi_1.14.1  rlecuyer_0.3-1
> [13] snow_0.3-5            qpgraph_1.8.0         multicore_0.1-5
> [16] Biobase_2.12.1        graph_1.30.0          igraph_0.5.5-2
>
> loaded via a namespace (and not attached):
> [1] geneplotter_1.30.0 grid_2.13.0        Matrix_0.999375-50
> RColorBrewer_1.0-2
> [5] splines_2.13.0     survival_2.36-5    tcltk_2.13.0       xtable_1.5-6
>
>
>
>
>
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber