Using \'spliceIndex\' function from \'annmap\' package: How do I know what \'ids\' should be?
0
0
Entering edit mode
Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
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: read.celfiles(list.celfiles("/my/directory",fullnames=TRUE) 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: spliceIndex(rma.output,gps=list(1:3,4:6)) 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) locale: [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.
probe probe • 711 views
ADD COMMENT

Login before adding your answer.

Traffic: 458 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6