[BioC] Draft support for HTA 2.0 with oligo

[James W. MacDonald]

Hi Johann,

On 2/28/2014 12:05 PM, Johann Pellet wrote:
> 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

If I were to guess, I would bet that you built the package and then used 
something like WinZip to create a zip file.

If so, you can't do that. Instead you want to do

install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0", repos=NULL, type 
= "source")

Best,

Jim


>
>
>> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099