[BioC] Draft support for HTA 2.0 with oligo

[Johann Pellet]

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.