[BioC] problem with probes2tableBM
James W. MacDonald
jmacdon at med.umich.edu
Tue Sep 25 16:23:32 CEST 2007
Hi Mayte,
You have uncovered a bug in probes2tableBM(). I will fix this in the
devel version. I am in the process of setting up a new work computer, so
I am not able to check things out right now - when I am able I will see
if there is a quick workaround that will get you going right now.
Best,
Jim
Steffen wrote:
> Hi Mayte,
>
> The hgu133a2 chip has a different attribute and filter name in Ensembl
> and it looks like the probes2tableBM function assumes that the filter
> and attribute names are the same for every platform (ideally it should).
> The attribute name for this platform is affy_hg_u133a_v2 and the filter
> name is affy_hg_u133a_2. Maybe Jim can comment on how to get the
> function working in this case?
> Alternatively you can do your query using the getBM function instead of
> probes2tableBM.
>
> Cheers,
> Steffen
>
>
> Mayte Suarez-Farinas wrote:
>> Hi,
>>
>> I am having problems with function probes2tableBM again, and I can
>> not figure it out what is the right
>> ann.source for hgu133a2 chips. here is the code
>>
>>
>> > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
>> Checking attributes and filters ... ok
>>
>> > probes2tableBM(eset, probids=featureNames(eset)
>> [1:10],filename='llll',
>> + species="hsapiens",
>> ann.source="affy_hg_u133a_2", links=linksBM()[c(1:3)], otherann=annBM
>> ()[1:2], affyid=TRUE, express=FALSE)
>> connected to: ensembl
>> Reading database configuration of: hsapiens_gene_ensembl
>> Checking attributes and filters ... ok
>> Checking main tables ... ok
>> Error in getBM(attributes = links$links, filter = ann.source, values
>> = gn, :
>> Invalid attribute(s): affy_hg_u133a_2
>> Please use the function 'listAttributes' to get valid attribute names
>>
>>
>> when I do that:
>>
>> > listAttributes(mart_hs)[1:20,]
>> name description
>> 1 affy_hcg110 AFFY HCG110
>> 2 affy_hg_focus AFFY HG FOCUS
>> 3 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2
>> 4 affy_hg_u133a AFFY HG U133A
>> 5 affy_hg_u133a_v2 AFFY HG U133Av2
>> 6 affy_hg_u133b AFFY HG U133B
>> 7 affy_hg_u95a AFFY HG U95A
>> 8 affy_hg_u95av2 AFFY HG U95AV2
>> 9 affy_hg_u95b AFFY HG U95B
>> 10 affy_hg_u95c AFFY HG U95C
>> 11 affy_hg_u95d AFFY HG U95D
>> 12 affy_hg_u95e AFFY HG U95E
>> 13 affy_hugenefl AFFY HUGENEFL
>> 14 affy_u133_x3p AFFY U133 X3P
>> 15 agilent_cgh Agilent cgh
>> 16 agilent_probe Agilent Probe
>> 17 band Band
>> 18 biotype Biotype
>> 19 ccds CCDS ID
>> 20 chromosome_name Chromosome Name
>>
>>
>>
>> so I tried with ann.source=affy_hg_u133a_v2 but I get another error:
>>
>> > probes2tableBM(eset, probids=featureNames(eset)
>> [1:10],filename='llll',
>> + species="hsapiens",
>> ann.source="affy_hg_u133a_v2", links=linksBM()[c(1:3)], otherann=annBM
>> ()[1:2], affyid=TRUE, express=FALSE)
>> connected to: ensembl
>> Reading database configuration of: hsapiens_gene_ensembl
>> Checking attributes and filters ... ok
>> Checking main tables ... ok
>> Error: ' affy_hg_u133a_v2 'is not an available annotation source for
>> this biomaRt or this species.
>> Available choices are listed below:
>> name
>> description
>> 1 affy_hc_g110 Affy hc g 110
>> ID(s)
>> 2 affy_hg_focus Affy hg focus
>> ID(s)
>> 3 affy_hg_u133_plus_2 Affy hg u133 plus 2
>> ID(s)
>> 4 affy_hg_u133a Affy hg u133a
>> ID(s)
>> 5 affy_hg_u133a_2 Affy hg u133a 2
>> ID(s)
>> 6 affy_hg_u133b Affy hg u133b
>> ID(s)
>> 7 affy_hg_u95a Affy hg u95a
>> ID(s)
>> 8 affy_hg_u95av2 Affy hg u95av2
>> ID(s)
>> 9 affy_hg_u95b Affy hg u95b
>> ID(s)
>> 10 affy_hg_u95c Affy hg u95c
>> ID(s)
>> 11 affy_hg_u95d Affy hg u95d
>> ID(s)
>> 12 affy_hg_u95e Affy hg u95e
>> ID(s)
>> 13 affy_hugenefl Affy hugenefl
>> ID(s)
>> 14 affy_u133_x3p Affy u133 x3p
>> ID(s)
>> ............
>>
>>
>>
>> sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> i386-apple-darwin8.9.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] "splines" "tools" "stats" "graphics" "grDevices"
>> "utils" "datasets" "methods" "base"
>>
>> other attached packages:
>> RMySQL DBI affycoretools annaffy
>> xtable gcrma matchprobes biomaRt RCurl
>> "0.5-11" "0.2-2" "1.8.0" "1.8.1"
>> "1.4-3" "2.8.0" "1.8.1" "1.10.0" "0.8-0"
>> XML GOstats Category Matrix
>> lattice genefilter survival KEGG RBGL
>> "1.7-3" "2.2.1" "2.2.1" "0.9975-11"
>> "0.15-4" "1.14.1" "2.31" "1.15.13" "1.12.0"
>> annotate GO graph limma
>> affy affyio Biobase
>> "1.14.1" "1.16.0" "1.14.0" "2.10.0"
>> "1.14.0" "1.4.0" "1.14.0"
>>
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>>
>
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