Hello,

I am using Affymetrix Human Transcriptome Array (HTA) 2.0 Gene Chips and am having problems using the oligo package to do the data analysis.  After looking through the documentation and the other support questions, I haven't been able to find a solution.

Any tips or help with an HTA analysis pipeline?

Thanks,

Jen

> library(oligo)
> library(pd.hta.2.0)
> library(affy)

> celFiles<-list.celfiles()
> affyRaw<-read.celfiles(celFiles)
> class(affyRaw)
[1] "HTAFeatureSet"

attr(,"package")
[1] "oligoClasses"

> norm<-rma(affyRaw, target="probeset")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘probeNames’ for signature ‘"HTAFeatureSet"’

>norm<-rma(affyRaw, target="core")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘probeNames’ for signature ‘"HTAFeatureSet"’

> traceback()
4: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
       sQuote(fdef@generic), sQuote(cnames)), domain = NA)
3: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, 
               ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("HTAFeatureSet"), function (object, ...) 
   standardGeneric("probeNames"), <environment>)
2: probeNames(object, subset)
1: rma(affyRaw, target = "core")

------------------------------------------------------------------------------------------------------------------------------

> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] oligoData_1.8.0      affy_1.48.0          BiocInstaller_1.20.1 pd.hta.2.0_3.12.1    RSQLite_1.0.0       
 [6] DBI_0.3.1            oligo_1.34.2         Biostrings_2.38.4    XVector_0.10.0       IRanges_2.4.8       
[11] S4Vectors_0.8.11     Biobase_2.30.0       oligoClasses_1.32.0  BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] affxparser_1.42.0          GenomicRanges_1.22.4       splines_3.2.4              zlibbioc_1.16.0           
 [5] bit_1.1-12                 foreach_1.4.3              GenomeInfoDb_1.6.3         tools_3.2.4               
 [9] SummarizedExperiment_1.0.2 ff_2.2-13                  iterators_1.0.8            preprocessCore_1.32.0     
[13] affyio_1.40.0              codetools_0.2-14  

When you load the affy package after oligo, you mask the rma function in oligo (because affy has one as well). In that situation, you have to say which function you want.

norm <- oligo::rma(affyRaw)