Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
Entering edit mode
sorghills • 0
Last seen 5.2 years ago

Hello, everyone.

I'm trying to create an annotation package to use with Oligo in microarray analysis. I had provided the .xys file and a .ndf file as requested and I received the following error:

Building annotation package for Nimblegen Expression Array
NDF: GPL10191_090828_HG18.ndf
XYS: GSM597196_Nimblegen_Human_12-plex_434164_A12_MB6_.xys
Parsing file: GPL10191_090828_HG18.ndf... OK
Parsing file: GSM597196_Nimblegen_Human_12-plex_434164_A12_MB6_.xys... OK
Merging NDF and XYS files... OK
Preparing contents for featureSet table... OK
Preparing contents for bgfeature table... OK
Preparing contents for pmfeature table... OK
Error in parseNgsPair(object@ndfFile, object@xysFile, verbose = !quiet) :
  Control probe possibly identified as Experimental

I already checked if the files had unnecessary lines, restarted R, re-loaded only necessary packages, cleaned unused objects from environment, and double-checked code syntax.

Can anyone help me?

Thank you so much!


sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252 
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C 
[5] LC_TIME=Portuguese_Brazil.1252

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils 
[8] datasets methods base

other attached packages: [1] pdInfoBuilder_1.38.0 affxparser_1.46.0 RSQLite_1.1-2 
[4] HELP_1.32.0 Ringo_1.38.0 lattice_0.20-34 
[7] Matrix_1.2-8 limma_3.30.11 RColorBrewer_1.1-2 
[10] oligo_1.38.0 Biostrings_2.42.1 XVector_0.14.0 
[13] IRanges_2.8.1 S4Vectors_0.12.1 Biobase_2.34.0 
[16] oligoClasses_1.36.0 BiocGenerics_0.20.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.9 plyr_1.8.4 
[3] BiocInstaller_1.24.0 GenomeInfoDb_1.10.3 
[5] bitops_1.0-6 iterators_1.0.8 
[7] tools_3.3.2 zlibbioc_1.20.0 
[9] digest_0.6.12 bit_1.1-12 
[11] tibble_1.2 gtable_0.2.0 
[13] annotate_1.52.1 memoise_1.0.0 
[15] preprocessCore_1.36.0 ff_2.2-13 
[17] foreach_1.4.3 DBI_0.5-1 
[19] genefilter_1.56.0 AnnotationDbi_1.36.2 
[21] survival_2.40-1 XML_3.98-1.5 
[23] ggplot2_2.2.1 scales_0.4.1 
[25] codetools_0.2-15 GenomicRanges_1.26.2 
[27] splines_3.3.2 assertthat_0.1 
[29] SummarizedExperiment_1.4.0 colorspace_1.3-2 
[31] xtable_1.8-2 affy_1.52.0 
[33] lazyeval_0.2.0 munsell_0.4.3 
[35] RCurl_1.95-4.8 vsn_3.42.3 
[37] affyio_1.44.0


bioconductor pdfinfobuilder microarray nimblegene oligo • 565 views
Entering edit mode
sorghills • 0
Last seen 5.2 years ago

Hey there, I fixed it by editing the .ndf file and replacing some probe mismatch values from > 10000 to 0. Now, I'll filter those out, before analysis. 


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