Apologies if any of my questions are naīve, as I don't have a lot of experience with exon arrays.  I would like to analyze an Affy HuGene 1.0 ST array using the brainArray CDF (because I want to get expression values on a per gene level), and use fRMA (to correct for batch effects and enable me to add additional samples in the future without redoing RMA).  Is this possible?  Here's what I've tried without much success thus far:

I can skip brainarray and just load the data and run fRMA without error:
> exonFS <- read.celfiles(filenames=cel.files, verbose=F, celfile.path=NULL)
> tmp.eset <- frma(exonFS, summarize="median_polish")

But when I use ReadAffy and specify the cdf, fRMA generates an error:
> Affybatch <- ReadAffy(filenames=cel.files, verbose=F, celfile.path=NULL, cdfname="hugene10sthsentrezg")
Warning message:

The affy package can process data from the Gene ST 1.x series of arrays,
but you should consider using either the oligo or xps packages, which are specifically
designed for these arrays.

> tmp.eset <- frma(Affybatch, summarize="median_polish")
Error in frmaMedPol(object, background, normalize, target, input.vecs,  :
  hugene10stfrmavecs package must be installed first
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'hugene10stfrmavecs'


When I try running fRMA while directly passing the frmavecs to the function I get a different error:
> data(hugene.1.0.st.v1frmavecs)
> tmp.eset <- frma(Affybatch, summarize="median_polish", input.vecs=hugene.1.0.st.v1frmavecs)
Warning message:
In log2(pms) - input.vecs$probeVec :
  longer object length is not a multiple of shorter object length


Thanks in advance for any help,

Ty


> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

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] parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hugene10sthsentrezgcdf_17.1.0  AnnotationDbi_1.22.6           hugene.1.0.st.v1frmavecs_0.0.3 pd.hugene.1.0.st.v1_3.8.0
 [5] RSQLite_0.11.4                 DBI_0.2-7                      frma_1.12.0                    oligo_1.24.2
 [9] oligoClasses_1.22.0            affy_1.38.1                    Biobase_2.20.1                 BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.4  Biostrings_2.28.0     bit_1.1-11            codetools_0.2-8
 [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.12.5  IRanges_1.18.4        iterators_1.0.6       MASS_7.3-29
[13] preprocessCore_1.22.0 splines_3.0.1         stats4_3.0.1          tools_3.0.1           zlibbioc_1.6.0

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