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:
[1] 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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] hta20sttranscriptcluster.db_8.3.1 org.Hs.eg.db_3.3.0               
 [3] AnnotationDbi_1.35.4              AffyCompatible_1.33.0            
 [5] RCurl_1.95-4.8                    bitops_1.0-6                     
 [7] XML_3.98-1.4                      biomaRt_2.29.2                   
 [9] BiocInstaller_1.23.9              genefilter_1.55.2                
[11] pd.clariom.d.human_0.0.1          RSQLite_1.0.0                    
[13] DBI_0.5-1                         oligo_1.37.2                     
[15] Biostrings_2.41.4                 XVector_0.13.7                   
[17] IRanges_2.7.15                    S4Vectors_0.11.14                
[19] oligoClasses_1.35.0               limma_3.29.21                    
[21] Biobase_2.33.3                    BiocGenerics_0.19.2              

loaded via a namespace (and not attached):
 [1] GenomeInfoDb_1.9.10         iterators_1.0.8            
 [3] tools_3.3.1                 zlibbioc_1.19.0            
 [5] bit_1.1-12                  annotate_1.51.0            
 [7] preprocessCore_1.35.0       lattice_0.20-34            
 [9] ff_2.2-13                   Matrix_1.2-7.1             
[11] foreach_1.4.3               affxparser_1.45.0          
[13] grid_3.3.1                  survival_2.39-5            
[15] codetools_0.2-14            GenomicRanges_1.25.94      
[17] splines_3.3.1               SummarizedExperiment_1.3.82
[19] xtable_1.8-2                affyio_1.43.0              

 

The easiest thing to do for now is to use annotateEset in my affycoretools package. Something like

library(oligo)

library(affycoretools)

dat <- read.celfiles(list.celfiles())

eset <- rma(dat)

eset <- annotateEset(eset, pd.clariom.d.human)

head(fData(eset))