[BioC] vennSelect error

[James W. MacDonald]

Hi Mali,

On 6/2/2011 7:40 AM, mali salmon wrote:
> Dear list
> I am trying to use affycoretools for the analysis of affy yeast arrays.
> When I tried to use vennSelect in order generate HTML files containing the
> results of decideTests I got the following error:
>
>> annotation(eset)<-"yeast2.db"

Good thing you didn't snip the above line from your code. In the future, 
it is better to give us more than what you think we need, rather than less.

The problem here is that you are resetting the annotation slot for your 
ExpressionSet (unnecessarily, and incorrectly). Not sure why you are 
doing this; did you see some code somewhere that lead you to believe 
this is either desired or necessary? If so, please tell us so we can 
hopefully get it corrected.

Note that the annotation slot for an ExpressionSet doesn't imply 
annotation of (in this case) probeset IDs to genes, etc. The annotation 
slot contains name of the package that has the mappings of probes to 
probesets that were used to created the summarized values in that 
ExpressionSet. This is nice to have if you save the object, and wonder 
later how exactly the data were summarized.

So start back at the line preceding the line above where you reset the 
annotation slot, and try again, without resetting the annotation slot.

Best,

Jim


> ...
>> fit2<- eBayes(fit2)
>> results<- decideTests(fit2,lfc=1)
>> vennSelect(filtered,design,results,cont.matrix,fit2)
> Error in sqliteExecStatement(con, statement, bind.data) :
>    RS-DBI driver: (error in statement: cannot join using column gene_id -
> column not present in both tables)
>
> Any idea why I get this error?
> Thanks
> Mali
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-redhat-linux-gnu (32-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] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] hgu133a2.db_2.4.5    org.Hs.eg.db_2.4.6   annaffy_1.22.0
>   [4] affycoretools_1.22.0 KEGG.db_2.4.5        GO.db_2.4.5
>   [7] gplots_2.8.0         caTools_1.11         bitops_1.0-4.1
> [10] gdata_2.8.1          gtools_2.6.2         yeast2.db_2.4.5
> [13] org.Sc.sgd.db_2.4.6  RSQLite_0.9-4        DBI_0.2-5
> [16] annotate_1.28.1      AnnotationDbi_1.12.0 genefilter_1.32.0
> [19] yeast2cdf_2.7.0      affy_1.28.0          Biobase_2.10.0
> [22] limma_3.6.9
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.18.0         biomaRt_2.6.0         Biostrings_2.18.2
>   [4] Category_2.16.1       gcrma_2.22.0          GOstats_2.16.0
>   [7] graph_1.28.0          GSEABase_1.12.2       IRanges_1.8.9
> [10] preprocessCore_1.12.0 RBGL_1.26.0           RCurl_1.5-0
> [13] splines_2.12.1        survival_2.36-2       tcltk_2.12.1
> [16] tools_2.12.1          XML_3.2-0             xtable_1.5-6
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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