After building the package, as you showed on your email, you should be able
to install it just by using:

install.packages('pd.hta.2.0', repo=NULL)

Then, for reading the celfiles, do not give a txt file as input for
phenoData. I may need to fix the code, but in the meantime use something
like:

library(oligo)
cels = list.files()
raw = read.celfiles(cels)
pd = read.AnnotatedDataFrame('Raw/phenodataHTA2.txt')
phenoData(raw) = pd

benilton


2014-02-28 14:05 GMT-03:00 Johann Pellet <jpellet@eisbm.org>:

> Dear Benilton,
>
> thanks for this first draft support for the HTA 2.0 chip.
>
> I tried to follow your workflow using your annotation package specific for
> HTA or one built through pdInfoBuilder.  For both I can not use the package
> pd.hta.2.0, see below.
>
> > library(oligo)
> > install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0.zip", repos = NULL)
> > library(pd.hta.2.0)
> Error in library(pd.hta.2.0) :
>   ëpd.hta.2.0í is not a valid installed package
>
>
> > raw = read.celfiles(phenoData="Raw/phenodataHTA2.txt",verbose=TRUE,
> filenames=cels)
> Loading required package: pd.hta.2.0
> Failed with error:  ëëpd.hta.2.0í is not a valid installed packageí
> Attempting to obtain 'pd.hta.2.0' from BioConductor website.
> Checking to see if your internet connection works...
> Package 'pd.hta.2.0' was not found in the BioConductor repository.
> The 'pdInfoBuilder' package can often be used in situations like this.
> Error in read.celfiles(phenoData = "Raw/phenodataHTA2.txt", verbose =
> TRUE,  :
>   The annotation package, pd.hta.2.0, could not be loaded.
>
>
> ###### More info
>
> > sessionInfo()
> R Under development (unstable) (2014-02-27 r65090)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] pdInfoBuilder_1.27.5 oligo_1.27.9         Biostrings_2.31.14
> XVector_0.3.7
>  [5] IRanges_1.21.32      oligoClasses_1.25.6  affxparser_1.35.0
>  RSQLite_0.11.4
>  [9] DBI_0.2-7            Biobase_2.23.5       BiocGenerics_0.9.3
> BiocInstaller_1.13.3
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.31.0         bit_1.1-11            codetools_0.2-8
> ff_2.2-12
>  [5] foreach_1.4.1         GenomicRanges_1.15.31 iterators_1.0.6
> preprocessCore_1.25.5
>  [9] splines_3.1.0         stats4_3.1.0          tools_3.1.0
> zlibbioc_1.9.0
> >
>
>
>
> > makePdInfoPackage(seed, destDir=".")
>
> =============================================================================================
> Building annotation package for Affymetrix HTA Array
> PGF.........: HTA-2_0.r1.pgf
> CLF.........: HTA-2_0.r1.clf
> Probeset....: HTA-2_0.na33.hg19.probeset.csv
> Transcript..: HTA-2_0.na33.hg19.transcript.csv
> Core MPS....: HTA-2_0.r1.Psrs.mps
>
> =============================================================================================
> Parsing file: HTA-2_0.r1.pgf... OK
> Parsing file: HTA-2_0.r1.clf... OK
> Creating initial table for probes... OK
> Creating dictionaries... OK
> Parsing file: HTA-2_0.na33.hg19.probeset.csv... OK
> Parsing file: HTA-2_0.r1.Psrs.mps... OK
> Creating package in ./pd.hta.2.0
> Inserting 850 rows into table chrom_dict... OK
> Inserting 5 rows into table level_dict... OK
> Inserting 14 rows into table type_dict... OK
> Inserting 577432 rows into table core_mps... OK
> Inserting 925032 rows into table featureSet... OK
> Inserting 7576209 rows into table pmfeature... OK
> Inserting 1121 rows into table mmfeature... OK
> Counting rows in chrom_dict
> Counting rows in core_mps
> Counting rows in featureSet
> Counting rows in level_dict
> Counting rows in mmfeature
> Counting rows in pmfeature
> Counting rows in type_dict
> Creating index idx_pmfsetid on pmfeature... OK
> Creating index idx_pmfid on pmfeature... OK
> Creating index idx_fsfsetid on featureSet... OK
> Creating index idx_core_meta_fsetid on core_mps... OK
> Creating index idx_core_fsetid on core_mps... OK
> Creating index idx_mmfsetid on mmfeature... OK
> Creating index idx_mmfid on mmfeature... OK
> Saving DataFrame object for PM.
> Saving DataFrame object for MM.
> Saving NetAffx Annotation... OK
> Done.
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