Hi,

I am trying to make a pd.info package for the Affy Primeview array, but I
get an error.

Thanks for any help!

Cheers,

Max

 

 

This is my code:

 

library(pdInfoBuilder)

cdf <- list.files( pathAnnotPr, pattern = ".cdf", full.names = TRUE )

cel <- list.files( pathC, pattern = ".CEL", full.names = TRUE )[1] #  take
first array

tab <- list.files(pathAnnotPr, pattern = "_tab", full.names = TRUE)

 

seed <- new("AffyExpressionPDInfoPkgSeed",

      cdfFile = cdf, celFile = cel,

      tabSeqFile = tab, author = "xx",

      email = "xx",

      biocViews = "AnnotationData",

      genomebuild = "hg19",

      organism = "Human", species = "Homo Sapiens",

      url = "xx"

)

makePdInfoPackage( seed, destDir = "." )

 

 

 

Which produces this output/error (although a pd.primeview directory is
created):

 

============================================================================
====

Building annotation package for Affymetrix Expression array

CDF...............:  PrimeView.cdf 

CEL...............:  MJ_05042013_TAS_10_PrimeView.CEL 

Sequence TAB-Delim:  PrimeView.probe_tab 

============================================================================
====

Parsing file: PrimeView.cdf... OK

Parsing file: MJ_05042013_TAS_10_PrimeView.CEL... OK

Parsing file: PrimeView.probe_tab... OK

Getting information for featureSet table... OK

Getting information for pm/mm feature tables... 

OK

Combining probe information with sequence information... OK

Getting PM probes and sequences... OK

Done parsing.

Creating package in ./pd.primeview 

Inserting 49395 rows into table featureSet... OK

Inserting 609663 rows into table pmfeature... Error in
sqliteExecStatement(con, statement, bind.data) : 

  RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be
unique)

In addition: Warning messages:

1: In parseCdfCelProbe(object@cdfFile, object@celFile, object@tabSeqFile,  :

  Probe sequences were not found for all PM probes. These probes will be
removed from the pmSequence object.

2: In parseCdfCelProbe(object@cdfFile, object@celFile, object@tabSeqFile,  :

  Probe sequences were not found for all MM probes. These probes will be
removed from the mmSequence object.

 

 

 

> sessionInfo()

R version 3.0.0 (2013-04-03)

Platform: x86_64-unknown-linux-gnu (64-bit)

 

locale:

[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=C                 LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

 

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     

 

other attached packages:

[1] pdInfoBuilder_1.24.0 oligo_1.24.0         oligoClasses_1.22.0 

[4] affxparser_1.32.1    RSQLite_0.11.4       DBI_0.2-7           

[7] Biobase_2.20.0       BiocGenerics_0.6.0  

 

loaded via a namespace (and not attached):

[1] affyio_1.28.0         BiocInstaller_1.10.2  Biostrings_2.28.0    

 [4] bit_1.1-10            codetools_0.2-8       ff_2.2-11            

 [7] foreach_1.4.1         GenomicRanges_1.12.4  IRanges_1.18.1       

[10] iterators_1.0.6       preprocessCore_1.22.0 splines_3.0.0        

[13] stats4_3.0.0          zlibbioc_1.6.0       

> 

 

Max Kauer 

CHILDREN'S CANCER RESEARCH INSTITUTE

 


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