I am having trouble figuring out how to transform the probeset ID from the Affy given name to an entrez ID (heck, I would even settle for gene symbols). My session info is listed at the bottom of this post. I run into this problem whether utilizing the custom CDF that was given to me by Affymetrix, or utilizing pdInfoMaker as was described C: Clariom D Human Microarray CDF file to package. Just as there is no CDF publicly available, there is no annotation .db object available.
I have tried the 'AffyCompatable' package to fetch the NetAffx resource, however, it returns a data frame with all the information jumbled into a single column.
I have also tried utilizing the .db for the predecessor, just to be able to match the Affy_id's to the entrez Id's but that returns an error.
> library(hta20sttranscriptcluster.db) Loading required package: org.Hs.eg.db > affyid <- rownames(eset) > egids2 <- hta20sttranscriptclusterENTREZID[affyid] Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "AFFX-BkGr-GC03_st" not found
My session info. Can you tell I have been trying a ton of different things?
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan) 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:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  hta20sttranscriptcluster.db_8.3.1 org.Hs.eg.db_3.3.0  AnnotationDbi_1.35.4 AffyCompatible_1.33.0  RCurl_1.95-4.8 bitops_1.0-6  XML_3.98-1.4 biomaRt_2.29.2  BiocInstaller_1.23.9 genefilter_1.55.2  pd.clariom.d.human_0.0.1 RSQLite_1.0.0  DBI_0.5-1 oligo_1.37.2  Biostrings_2.41.4 XVector_0.13.7  IRanges_2.7.15 S4Vectors_0.11.14  oligoClasses_1.35.0 limma_3.29.21  Biobase_2.33.3 BiocGenerics_0.19.2 loaded via a namespace (and not attached):  GenomeInfoDb_1.9.10 iterators_1.0.8  tools_3.3.1 zlibbioc_1.19.0  bit_1.1-12 annotate_1.51.0  preprocessCore_1.35.0 lattice_0.20-34  ff_2.2-13 Matrix_1.2-7.1  foreach_1.4.3 affxparser_1.45.0  grid_3.3.1 survival_2.39-5  codetools_0.2-14 GenomicRanges_1.25.94  splines_3.3.1 SummarizedExperiment_1.3.82  xtable_1.8-2 affyio_1.43.0