[BioC] vennSelect error
James W. MacDonald
jmacdon at med.umich.edu
Thu Jun 2 21:36:12 CEST 2011
Hi Mali,
On 6/2/2011 3:00 PM, mali salmon wrote:
> 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)
The problem is that you are by default trying to get annotation for
> aaf.handler()[c(1:3,6:7, 9:12)]
[1] "Probe" "Symbol" "Description" "GenBank"
[5] "Gene" "UniGene" "PubMed" "Gene Ontology"
[9] "Pathway"
But since this is a yeast chip, not all of these are available. For this
sort of issue I have included a '...' argument to vennSelect() that
allows you to pass arguments to lower level functions, so you can just
do something like
library(annaffy) ## we need this to expose the aaf.handler() function
vennSelect(filtered, design, results, cont.matrix, fit2, anncols =
aaf.handler(chip = "yeast2.db"))
Which will then give you all possible annotations for the yeast2.db
chip, which are
> aaf.handler(chip = "yeast2.db")
[1] "Probe" "Description" "Chromosome"
[4] "Chromosome Location" "PubMed" "Gene Ontology"
[7] "Pathway"
Unfortunately, you will still get the error you see, which comes from
the call for Gene Ontology data, so if you amend to
vennSelect(filtered, design, results, cont.matrix, fit2, anncols =
aaf.handler(chip = "yeast2.db")[-6])
Then it will work. I will contact Colin Smith, the maintainer of
annaffy, separately to see if he can track down the error you see with
GO terms.
Best,
Jim
>
> 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 at 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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>
>
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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