[BioC] problem with probes2tableBM

Mayte Suarez-Farinas farinam at mail.rockefeller.edu
Mon Sep 24 22:32:32 CEST 2007


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"



More information about the Bioconductor mailing list