[BioC] Using \'spliceIndex\' function from \'annmap\' package: How do I know what \'ids\' should be?

Heather [guest] guest at bioconductor.org
Sat Mar 29 01:03:29 CET 2014

I have cel files from Affymetrix Human Exon 1.0 arrays: 3 treated and 3 control. The files are being read together, using 'aroma.affymetrix', 'oligo', and 'pd.huex.1.0.st.v2' packages:


I then used 'rma' (at the probe set level) on the raw cel files. I am now trying to use the 'spliceIndex' from 'annmap' package. I have so far:


But I am not sure what to put for 'ids'. The help package says ids is "Character vector of Ensembl gene names" but I am not exactly sure what that is, or where I get/make that vector. So, I am not able to run the 'spliceIndex' function.

Any help is greatly appreciated.

 -- output of sessionInfo(): 

R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] Rcpp_0.11.1             inline_0.3.13          
 [3] annmap_1.4.1            GenomicRanges_1.14.4   
 [5] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4         
 [7] DBI_0.2-7               Biostrings_2.30.1      
 [9] XVector_0.2.0           Biobase_2.22.0         
[11] oligoClasses_1.24.0     BiocGenerics_0.8.0     
[13] aroma.light_1.32.0      matrixStats_0.8.14     
[15] aroma.affymetrix_2.12.0 aroma.core_2.12.1      
[17] R.devices_2.8.2         R.filesets_2.4.0       
[19] R.utils_1.29.8          R.oo_1.18.0            
[21] oligo_1.26.6            affxparser_1.34.2      
[23] IRanges_1.20.7          R.methodsS3_1.6.1      
[25] BiocInstaller_1.12.0   

loaded via a namespace (and not attached):
 [1] affyio_1.30.0         annotate_1.40.1       AnnotationDbi_1.24.0 
 [4] aroma.apd_0.5.0       base64enc_0.1-1       bit_1.1-11           
 [7] bitops_1.0-6          codetools_0.2-8       digest_0.6.4         
[10] DNAcopy_1.36.0        ff_2.2-12             foreach_1.4.1        
[13] genefilter_1.44.0     grid_3.0.3            iterators_1.0.6      
[16] lattice_0.20-27       preprocessCore_1.24.0 PSCBS_0.41.0         
[19] R.cache_0.9.2         R.huge_0.8.0          R.rsp_0.15.0         
[22] RMySQL_0.9-3          Rsamtools_1.14.3      splines_3.0.3        
[25] stats4_3.0.3          survival_2.37-7       tools_3.0.3          
[28] XML_3.95-0.2          xtable_1.7-3          zlibbioc_1.8.0       

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list