[BioC] PAIR files -- feature set table

FRANKLIN JOHNSON [guest] guest at bioconductor.org
Thu Jun 6 02:01:46 CEST 2013

Dear Maintainer,

I downloaded available NimbleGen 'single channel' 532.PAIR files for a custom built expression microarray from NCBI/GEO (GPL11164). However, I get an error message when I try to make the annotation for this platform using pdInfoBuild.

In pdInfoBuilder Reference Manual (June 5, 2013), under the NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, showClasses("Ngs.."), does not show a slot for this, only, XYS. Thus, I changed the .pair file extension to .xys.   

(ndf<- list.files(getwd(), pattern=".ndf", full.names=TRUE)) # read annotation file
[1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray Paper/Yanmin Microarray RAW/GPL11164.ndf"

(xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1])
[1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's Microarray Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys"

But, doing this resulted in an error message:
seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, author = "FJ", organism = "Apple", species = "Malus x Domestica cv.GD")

makePdInfoPackage(arrays, destDir = getwd())
Building annotation package for Nimblegen Expression Array
NDF: GPL11164.ndf
XYS: GSM618107_14418002_532.xys
Parsing file: GPL11164.ndf... OK
Parsing file: GSM618107_14418002_532.xys... OK
Merging NDF and XYS files... OK
Preparing contents for featureSet table... Error in `[.data.frame`(ndfdata, , colsFS) : undefined columns selected
In addition: Warning message:
In is.na(ndfdata[["SIGNAL"]]) :
  is.na() applied to non-(list or vector) of type 'NULL'

The only files available from NCBI/GEO are 24 PAIR files and 1 ndf. It seems .xys has a different arrangement than .pair, thus .ndf is not applicable to annotate the .pair file? Any suggestions?
Hope to hear from you soon.

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] pdInfoBuilder_1.24.0 oligo_1.24.0         oligoClasses_1.22.0  affxparser_1.32.1    RSQLite_0.11.4       DBI_0.2-7           
 [7] Mfuzz_2.18.0         DynDoc_1.38.0        widgetTools_1.38.0   e1071_1.6-1          class_7.3-7          gplots_2.11.0.1     
[13] KernSmooth_2.23-10   caTools_1.14         gdata_2.12.0.2       gtools_2.7.1         timecourse_1.32.0    MASS_7.3-26         
[19] Biobase_2.20.0       BiocGenerics_0.6.0   limma_3.16.5         ggplot2_0.9.3.1      BiocInstaller_1.10.1

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         Biostrings_2.28.0     bit_1.1-10            bitops_1.0-5          codetools_0.2-8       colorspace_1.2-2     
 [7] dichromat_2.0-0       digest_0.6.3          ff_2.2-11             foreach_1.4.0         GenomicRanges_1.12.4  gtable_0.1.2         
[13] IRanges_1.18.1        iterators_1.0.6       labeling_0.1          marray_1.38.0         munsell_0.4           plyr_1.8             
[19] preprocessCore_1.22.0 proto_0.3-10          RColorBrewer_1.0-5    reshape2_1.2.2        scales_0.2.3          splines_3.0.1        
[25] stats4_3.0.1          stringr_0.6.2         tkWidgets_1.38.0      tools_3.0.1           zlibbioc_1.6.0       

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