Entering edit mode
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"