[BioC] problem with probes2tableBM

[Steffen]

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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