[BioC] PAIR files -- feature set table
Benilton Carvalho
beniltoncarvalho at gmail.com
Thu Jun 6 03:42:59 CEST 2013
It's an unfortunate mistake to have the pairFile *argument* in the
call (not in the slots session, but I see your point). :-( I'll make
sure that this is fixed.
You need to convert the PAIR files to XYS...
Some refs that should help you in the process:
https://stat.ethz.ch/pipermail/bioconductor/2012-January/043186.html
http://comments.gmane.org/gmane.science.biology.informatics.conductor/27547
b
2013/6/5 FRANKLIN JOHNSON [guest] <guest at bioconductor.org>:
>
> 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.
> Franklin
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [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
>>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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