[BioC] Cannot find the package created by pdInfoBuilder package

dhivya [guest] guest at bioconductor.org
Fri Mar 28 20:45:22 CET 2014


I’ m a bioinformatician at UT Austin and I’m trying to do time series analysis of an arabidopsis tiling array.  I used the makePdInfoPackage function to create a pdinfpackage using my bpmap files.  It worked successfully and I can see a directory called pd.at35b.mr.v04:

ls pd.at35b.mr.v04/
data  DESCRIPTION  inst  man  NAMESPACE  R

For further analysis, I need to provide the name of the "package containing the array probe and annotation information, as produces by the pdInfoBuilder-package".  Just providing the name of this directory does not seem to work (no such package error). Do I need to do some installation or additional step after creating this package, to use it?  I’m having difficulty finding this from the documentation and any help would be really appreciated.

thanks for any help
dhivya arasappan
UT Austin

 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] pdInfoBuilder_1.22.0                 affxparser_1.30.2                   
 [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1                     
 [5] GenomicRanges_1.10.7                 pd.atdschip.tiling_0.0.4            
 [7] RSQLite_0.11.4                       DBI_0.2-7                           
 [9] waveTilingData_0.99.1                waveTiling_1.0.0                    
[11] GenomeGraphs_1.18.0                  biomaRt_2.14.0                      
[13] Biostrings_2.26.3                    IRanges_1.16.6                      
[15] oligo_1.22.0                         Biobase_2.18.0                      
[17] oligoClasses_1.20.0                  BiocGenerics_0.4.0                  
[19] R.utils_1.29.8                       R.oo_1.18.0                         
[21] R.methodsS3_1.6.1                   

loaded via a namespace (and not attached):
 [1] affy_1.36.1           affyio_1.26.0         BiocInstaller_1.8.3  
 [4] bit_1.1-11            codetools_0.2-8       ff_2.2-12            
 [7] foreach_1.4.1         iterators_1.0.6       parallel_2.15.3      
[10] preprocessCore_1.20.0 RCurl_1.95-4.1        splines_2.15.3       
[13] stats4_2.15.3         waveslim_1.7.3        XML_3.98-1.1         
[16] zlibbioc_1.4.0       

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