Thanks Jim for your reply.
I repeated the analysis without resetting the annotation slot but I still
get the same error.
Below is the code I used:

>library(limma)
>library(affy)
>library(affycoretools)
>data <- ReadAffy()
>eset <- rma(data)
>#remove low variance genes
>library(genefilter)
>eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1)
>#remove control probes (AFFX)
>filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F)
>targets<-readTargets("targets.txt")
>TS <- paste(targets$Strain, targets$Treatment, sep=".")
>Strain <- factor(targets$Strain, levels=c("WT","Mu"))
>Treatment <- factor(targets$Treatment, levels=c("U","S"))
>design <- model.matrix(~Strain*Treatment)
>fit <- lmFit(filtered, design)
>cont.matrix <- cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1))
>fit2 <- contrasts.fit(fit, cont.matrix)
>fit2 <- eBayes(fit2)
>results <- decideTests(fit2,lfc=1)
>vennSelect(filtered, design, results, cont.matrix, fit2)

Loading required package: yeast2.db
Loading required package: org.Sc.sgd.db
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)

Thanks
Mali



On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote:

> 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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